基因渗入的检测和表征方法

doi:10.16288/j.yczz.22-394

遗传 ›› 2023, Vol. 45 ›› Issue (2): 128-143.doi: 10.16288/j.yczz.22-394

基因渗入的检测和表征方法

刘泽璇(), 赵毅强()

中国农业大学生物学院，北京 100193

收稿日期:2022-12-01 修回日期:2023-01-04 出版日期:2023-02-20 发布日期:2023-01-26
通讯作者: 赵毅强 E-mail:liuzexuan@cau.edu.cn;yiqiangz@cau.edu.cn
作者简介:刘泽璇，在读博士研究生，专业方向：生物信息学。E-mail: liuzexuan@cau.edu.cn
基金资助:
国家重点研发计划项目(2021YFD1200803);Supported by the National Key Research and Development Program of China No(2021YFD1200803)

Methods to detect and characterize introgression

Zexuan Liu(), Yiqiang Zhao()

College of Biological Sciences, China Agricultural University, Beijing 100193, China

Received:2022-12-01 Revised:2023-01-04 Online:2023-02-20 Published:2023-01-26
Contact: Zhao Yiqiang E-mail:liuzexuan@cau.edu.cn;yiqiangz@cau.edu.cn

摘要/Abstract

摘要：

基因渗入也称为渗入性杂交，遗传学上指通过不断回交，遗传成分从一个群体的基因库流向另一个群体基因库的过程。基因渗入在自然界广泛存在，对于增加遗传多样性和提高环境适应性起到了重要的贡献，影响着动植物以及人类的演化进程。基因渗入作为进化中的重要事件而被广泛关注，包括鉴定基因渗入是否发生以及渗入的方向、时间和渗入模式等。随着高通量测序技术的快速发展，使得利用全基因组数据检测和表征基因渗入的方法不断出现。本文系统总结了基因渗入检测的系列方法，介绍了这些方法的设计原理和使用案例，并讨论了渗入后基因片段的维持与选择，以期为基因渗入相关研究提供较为全面的参考。

关键词: 基因渗入, 渗入检测, 渗入方向, 渗入时间, 适应性渗入

Abstract:

Introgression, also known as introgressive hybridization, refers to the process that genetic components from the gene pool of one population transfer to the other via constant backcrossing. Introgression is widespread in nature, which plays important roles in increasing genetic diversity and improving adaptability to the environment, and in turn, influences the evolutionary progress of animals, plants and humans. Being as an important evolutionary event, researchers pay great attention to the detection of introgression, the introgression direction, the introgression timing, the pattern of introgression and so on. With the rapid development of high-throughput sequencing technologies, methods to detect and characterize introgression based on genome-wide data are continuously developed. In this review, we summarize a series of methods for introgression detection, and introduce the design principles and applications of these methods. We also discuss the maintenance and selection of gene segments after introgression. This review provides a relatively comprehensive reference for the studies on introgression.

Key words: introgression, introgression detection, introgression direction, introgression timing, adaptive introgression

刘泽璇, 赵毅强. 基因渗入的检测和表征方法[J]. 遗传, 2023, 45(2): 128-143.

Zexuan Liu, Yiqiang Zhao. Methods to detect and characterize introgression[J]. Hereditas(Beijing), 2023, 45(2): 128-143.

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参考文献 96

[1]	Rhymer JM, Simberloff D. Extinction by hybridization and introgression. Annu Rev Ecol Syst, 1996, 27: 83-109.
[2]	Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol, 2009, 24(7): 386-393. doi: 10.1016/j.tree.2009.02.011 pmid: 19409650
[3]	Anderson E. Introgressive hybridization. Biol Rev Camb Philos Soc, 1953, 28(3): 280-307. doi: 10.1111/j.1469-185X.1953.tb01379.x
[4]	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 K, 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
[5]	Zheng ZQ, Wang XH, Li M, Li YJ, Yang ZR, Wang XL, Pan XY, Gong M, Zhang Y, Guo YW, Wang Y, Liu J, Cai YD, Chen QM, Okpeku M, Colli L, Cai DW, Wang K, Huang SS, Sonstegard TS, Esmailizadeh A, Zhang WG, Zhang TT, Xu YB, Xu NY, Yang Y, Han JL, Chen L, Lesur J, Daly KG, Bradley DG, Heller R, Zhang GJ, Wang W, Chen YL, Jiang Y. The origin of domestication genes in goats. Sci Adv, 2020, 6(21): eaaz5216. doi: 10.1126/sciadv.aaz5216
[6]	Suarez-Gonzalez A, Hefer CA, Christe C, Corea O, Lexer C, Cronk QCB, Douglas CJ. Genomic and functional approaches reveal a case of adaptive introgression from populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood). Mol Ecol, 2016, 25(11): 2427-2442. doi: 10.1111/mec.13539 pmid: 26825293
[7]	Adavoudi R, Pilot M. Consequences of hybridization in mammals: a systematic review. Genes (Basel), 2021, 13(1): 50. doi: 10.3390/genes13010050
[8]	Suarez-Gonzalez A, Lexer C, Cronk QCB. Adaptive introgression: a plant perspective. Biol Lett, 2018, 14(3): 20170688. doi: 10.1098/rsbl.2017.0688
[9]	Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife, 2021, 10: e69016. doi: 10.7554/eLife.69016
[10]	Prüfer K, De Filippo C, Grote S, Mafessoni F, Korlevic P, Hajdinjak M, Vernot B, Skov L, Hsieh PS, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu QM, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage neandertal genome from vindija cave in croatia. Science, 2017, 358(6363): 655-658. doi: 10.1126/science.aao1887 pmid: 28982794
[11]	Baack EJ, Rieseberg LH. A genomic view of introgression and hybrid speciation. Curr Opin Genet Dev, 2007, 17(6): 513-518. doi: 10.1016/j.gde.2007.09.001 pmid: 17933508
[12]	Arnold ML. Transfer and origin of adaptations through natural hybridization: were anderson and stebbins right? Plant Cell, 2004, 16(3): 562-570. doi: 10.1105/tpc.160370 pmid: 15004269
[13]	Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol, 2019, 3(2): 170-177. doi: 10.1038/s41559-018-0777-y pmid: 30697003
[14]	Lexer C, Widmer A. The genic view of plant speciation: recent progress and emerging questions. Philos Trans R Soc Lond B Biol Sci, 2008, 363(1506): 3023-3036. doi: 10.1098/rstb.2008.0078
[15]	Mallet J, Besansky N, Hahn MW. How reticulated are species? Bioessays, 2016, 38(2): 140-149. doi: 10.1002/bies.201500149 pmid: 26709836
[16]	Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J, Good JM. Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science, 2018, 360(6395): 1355-1358. doi: 10.1126/science.aar5273 pmid: 29930138
[17]	Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol, 2016, 25(11): 2337-2360. doi: 10.1111/mec.13557 pmid: 26836441
[18]	Gompert Z, Mandeville EG, Buerkle CA. Analysis of population genomic data from hybrid zones. Annu Rev Ecol Syst, 2017, 48(1): 207-229.
[19]	Hibbins MS, Hahn MW. Phylogenomic approaches to detecting and characterizing introgression. Genetics, 2022, 220(2): iyab173. doi: 10.1093/genetics/iyab173
[20]	Yuan K, Zhou Y, Ni XM, Wang YC, Liu C, Xu SH. Models, methods and tools for ancestry inference and admixture analysis. Quant Biol, 2017, 5(3): 236-250. doi: 10.1007/s40484-017-0117-2
[21]	Jiao XY, Flouri T, Yang ZH. Multispecies coalescent and its applications to infer species phylogenies and cross- species gene flow. Natl Sci Rev, 2021, 8(12): nwab127. doi: 10.1093/nsr/nwab127
[22]	Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, Garcia-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, Di Palma F, 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
[23]	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
[24]	Bosse M, Megens HJ, Frantz LAF, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans RPMA, Groenen MAM. Genomic analysis reveals selection for asian genes in european pigs following human-mediated introgression. Nat Commun, 2014, 5: 4392. doi: 10.1038/ncomms5392 pmid: 25025832
[25]	Giuffra E, Kijas JM, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 2000, 154(4): 1785-1791. doi: 10.1093/genetics/154.4.1785 pmid: 10747069
[26]	Wang XT, Chen LY, Ma JX. Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication. Genome Biol, 2019, 20(1): 22. doi: 10.1186/s13059-019-1631-5 pmid: 30700312
[27]	Martin SH, Davey JW, Jiggins CD. Evaluating the use of ABBA-BABAa statistics to locate introgressed loci. Mol Biol Evol, 2015, 32(1): 244-257. doi: 10.1093/molbev/msu269 pmid: 25246699
[28]	Zhang CY, Lin D, Wang YZ, Peng DZ, Li HF, Fei J, Chen KW, Yang N, Hu XX, Zhao YQ, Li N. Widespread introgression in chinese indigenous chicken breeds from commercial broiler. Evol Appl, 2019, 12(3): 610-621. doi: 10.1111/eva.12742 pmid: 30828377
[29]	Wang YZ, Zhang CY, Peng YB, Cai XY, Hu XX, Bosse M, Zhao YQ. Whole-genome analysis reveals the hybrid formation of chinese indigenous DHB pig following human migration. Evol Appl, 2022, 15(3): 501-514. doi: 10.1111/eva.13366 pmid: 35386394
[30]	Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, Zhao JY, Zhuang Y, Xu X, Yamaguchi N, Driscoll CA, O'brien SJ, Luo SJ. Genomic evidence for the chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats. Sci Adv, 2021, 7(26): eabg0221. doi: 10.1126/sciadv.abg0221
[31]	Durand EY, Patterson N, Reich D, Slatkin M. Testing for ancient admixture between closely related populations. Mol Biol Evol, 2011, 28(8): 2239-2252. doi: 10.1093/molbev/msr048 pmid: 21325092
[32]	Patterson N, Moorjani P, Luo YT, Mallick S, Rohland N, Zhan YP, Genschoreck T, Webster T, Reich D. Ancient admixture in human history. Genetics, 2012, 192(3): 1065-1093. doi: 10.1534/genetics.112.145037 pmid: 22960212
[33]	Harris AM, Degiorgio M. Admixture and ancestry inference from ancient and modern samples through measures of population genetic drift. Hum Biol, 2017, 89(1): 21-46. pmid: 29285965
[34]	Zheng YC, Janke A. Gene flow analysis method, the D-statistic, is robust in a wide parameter space. BMC Bioinformatics, 2018, 19(1): 10. doi: 10.1186/s12859-017-2002-4 pmid: 29310567
[35]	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
[36]	Reich D, Thangaraj K, Patterson N, Price AL, Singh L. Reconstructing indian population history. Nature, 2009, 461(7263): 489-494. doi: 10.1038/nature08365
[37]	Martin SH, Davey JW, Salazar C, Jiggins CD. Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol, 2019, 17(2): e2006288. doi: 10.1371/journal.pbio.2006288
[38]	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
[39]	Vahedi SM, Ardestani SS, Afshari KP, Ghoreishifar SM, Moghaddaszadeh-Ahrabi S, Banabazi MH, Brito LF. Genome-wide selection signatures and human-mediated introgression events in Bos taurus indicus-influenced composite beef cattle. Front Genet, 2022, 13: 844653. doi: 10.3389/fgene.2022.844653
[40]	Hamlin JAP, Hibbins MS, Moyle LC. Assessing biological factors affecting postspeciation introgression. Evol Lett, 2020, 4(2): 137-154. doi: 10.1002/evl3.159 pmid: 32313689
[41]	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
[42]	Martin SH, Amos W. Signatures of introgression across the allele frequency spectrum. Mol Biol Evol, 2021, 38(2): 716-726. doi: 10.1093/molbev/msaa239 pmid: 32941617
[43]	Wang MS, Murray GGR, Mann D, Groves P, Vershinina AO, Supple MA, Kapp JD, Corbett-Detig R, Crump SE, Stirling I, Laidre KL, Kunz M, Dalén L, Green RE, Shapiro B. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nat Ecol Evol, 2022, 6(7): 936-944. doi: 10.1038/s41559-022-01753-8
[44]	Hibbins MS, Hahn MW. The timing and direction of introgression under the multispecies network coalescent. Genetics, 2019, 211(3): 1059-1073. doi: 10.1534/genetics.118.301831 pmid: 30670542
[45]	Forsythe ES, Sloan DB, Beilstein MA. Divergence-based introgression polarization. Genome Biol Evol, 2020, 12(4): 463-478.
[46]	Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of drosophila simulans and D. sechellia. PLoS Genet, 2018, 14(4): e1007341.
[47]	Joly S, Mclenachan PA, Lockhart PJ. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am Nat, 2009, 174(2): E54-E70. doi: 10.1086/600082
[48]	Geneva AJ, Muirhead CA, Kingan SB, Garrigan D. A new method to scan genomes for introgression in a secondary contact model. PLoS One, 2015, 10(4): e0118621. doi: 10.1371/journal.pone.0118621
[49]	Hudson RR. A new statistic for detecting genetic differentiation. Genetics, 2000, 155(4): 2011-2014. doi: 10.1093/genetics/155.4.2011 pmid: 10924493
[50]	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 pmid: 2513255
[51]	Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics, 1992, 132(2): 583-589. doi: 10.1093/genetics/132.2.583 pmid: 1427045
[52]	Dannemann M, Andrés AM, Kelso J. Introgression of neandertal- and denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. Am J Hum Genet, 2016, 98(1): 22-33. doi: 10.1016/j.ajhg.2015.11.015 pmid: 26748514
[53]	Hellenthal G, Busby GBJ, Band G, Wilson JF, Capelli C, Falush D, Myers S. A genetic atlas of human admixture history. Science, 2014, 343(6172): 747-751. doi: 10.1126/science.1243518 pmid: 24531965
[54]	Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet, 2012, 8(1): e1002453. doi: 10.1371/journal.pgen.1002453
[55]	Chimusa ER, Defo J, Thami PK, Awany D, Mulisa DD, Allali I, Ghazal H, Moussa A, Mazandu GK. Dating admixture events is unsolved problem in multi-way admixed populations. Brief Bioinform, 2020, 21(1): 144-155.
[56]	Hill WG, Robertson A. The effect of linkage on limits to artificial selection. Genet Res, 1966, 8(3): 269-294. doi: 10.1017/S0016672300010156
[57]	Winkler CA, Nelson GW, Smith MW. Admixture mapping comes of age. Annu Rev Genomics Hum Genet, 2010, 11: 65-89. doi: 10.1146/annurev-genom-082509-141523 pmid: 20594047
[58]	Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D. The history of african gene flow into southern europeans, levantines, and jews. PLoS Genet, 2011, 7(4): e1001373. doi: 10.1371/journal.pgen.1001373
[59]	Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring admixture histories of human populations using linkage disequilibrium. Genetics, 2013, 193(4): 1233-1254. doi: 10.1534/genetics.112.147330
[60]	Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D. Ancient west eurasian ancestry in southern and eastern africa. Proc Natl Acad Sci USA, 2014, 111(7): 2632-2637. doi: 10.1073/pnas.1313787111 pmid: 24550290
[61]	Busby GB, Band G, Le QS, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC,Malaria Genomic Epidemiology Network. Admixture into and within sub-saharan africa. eLife, 2016, 5: e15266.
[62]	Buerkle CA, Rieseberg LH. The rate of genome stabilization in homoploid hybrid species. Evolution, 2008, 62(2): 266-275. doi: 10.1111/j.1558-5646.2007.00267.x pmid: 18039323
[63]	Schumer M, Cui RF, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol, 2016, 25(11): 2661-2679. doi: 10.1111/mec.13602 pmid: 26937625
[64]	Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D. The genomic landscape of neanderthal ancestry in present-day humans. Nature, 2014, 507(7492): 354-357. doi: 10.1038/nature12961
[65]	Stukenbrock EH, Christiansen FB, Hansen TT, Dutheil JY, Schierup MH. Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc Natl Acad Sci USA, 2012, 109(27): 10954-10959. doi: 10.1073/pnas.1201403109 pmid: 22711811
[66]	Orr HA. The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics, 1995, 139(4): 1805-1813. doi: 10.1093/genetics/139.4.1805 pmid: 7789779
[67]	Schluter D. Evidence for ecological speciation and its alternative. Science, 2009, 323(5915): 737-741. doi: 10.1126/science.1160006 pmid: 19197053
[68]	Harris K, Nielsen R. The genetic cost of neanderthal introgression. Genetics, 2016, 203(2): 881-891. doi: 10.1534/genetics.116.186890 pmid: 27038113
[69]	Sankararaman S, Mallick S, Patterson N, Reich D. The combined landscape of denisovan and neanderthal ancestry in present-day humans. Curr Biol, 2016, 26(9): 1241-1247. doi: 10.1016/j.cub.2016.03.037 pmid: 27032491
[70]	Veller C, Edelman NB, Muralidhar P, Nowak MA. Recombination and selection against introgressed DNA. bioRxiv, 2021.
[71]	Kulmuni J, Nouhaud P, Pluckrose L, Satokangas I, Dhaygude K, Butlin RK. Instability of natural selection at candidate barrier loci underlying speciation in wood ants. Mol Ecol, 2020, 29(20): 3988-3999. doi: 10.1111/mec.15606
[72]	Vernot B, Akey JM. Resurrecting surviving neandertal lineages from modern human genomes. Science, 2014, 343(6174): 1017-1021. doi: 10.1126/science.1245938 pmid: 24476670
[73]	Petr M, Pääbo S, Kelso J, Vernot B. Limits of long-term selection against neandertal introgression. Proc Natl Acad Sci USA, 2019, 116(5): 1639-1644. doi: 10.1073/pnas.1814338116 pmid: 30647110
[74]	Barton NH, Otto SP. Evolution of recombination due to random drift. Genetics, 2005, 169(4): 2353-2370. pmid: 15687279
[75]	Juric I, Aeschbacher S, Coop G. The strength of selection against neanderthal introgression. PLoS Genet, 2016, 12(11): e1006340. doi: 10.1371/journal.pgen.1006340
[76]	Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, De Filippo C, Li H, Mallick S, Dannemann M, Fu QM, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a neanderthal from the altai mountains. Nature, 2014, 505(7481): 43-49. doi: 10.1038/nature12886
[77]	Milne RI, Abbott RJ. Origin and evolution of invasive naturalized material of Rhododendron ponticum L. In the british isles. Mol Ecol, 2000, 9(5): 541-556. doi: 10.1046/j.1365-294x.2000.00906.x pmid: 10792698
[78]	Ai HS, Fang XD, Yang B, Huang ZY, Chen H, Mao LK, Zhang F, Zhang L, Cui LL, He WM, Yang J, Yao XM, Zhou LS, Han LJ, Li J, Sun SL, Xie XH, Lai BX, Su Y, Lu Y, Yang H, Huang T, Deng WJ, Nielsen R, Ren J, Huang LS. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet, 2015, 47(3): 217-225. doi: 10.1038/ng.3199 pmid: 25621459
[79]	Zeberg H, Pääbo S. The major genetic risk factor for severe COVID-19 is inherited from neanderthals. Nature, 2020, 587(7835): 610-612. doi: 10.1038/s41586-020-2818-3
[80]	Shchur V, Svedberg J, Medina P, Corbett-Detig R, Nielsen R. On the distribution of tract lengths during adaptive introgression. G3 (Bethesda), 2020, 10(10): 3663-3673. doi: 10.1534/g3.120.401616
[81]	Edelman NB, Mallet J. Prevalence and adaptive impact of introgression. Annu Rev Genet, 2021, 55: 265-283. doi: 10.1146/annurev-genet-021821-020805 pmid: 34579539
[82]	Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He MZ, Somel M, Ni PX, Wang B, Ou XH, Huasang, Luosang JB, Cuo ZXP, Li K, Gao GY, Yin Y, Wang W, Zhang XQ, Xu X, Yang HM, Li YR, Wang J, Wang J, Nielsen R. Altitude adaptation in tibetans caused by introgression of denisovan-like DNA. Nature, 2014, 512(7513): 194-197. doi: 10.1038/nature13408
[83]	Vonholdt B, Fan ZX, Vecchyo DOD, Wayne RK. EPAS1 variants in high altitude tibetan wolves were selectively introgressed into highland dogs. PeerJ, 2017, 5: e3522. doi: 10.7717/peerj.3522
[84]	Wang MS, Wang S, Li Y, Jhala Y, Thakur M, Otecko NO, Si JF, Chen HM, Shapiro B, Nielsen R, Zhang YP, Wu DD. Ancient hybridization with an unknown population facilitated high-altitude adaptation of canids. Mol Biol Evol, 2020, 37(9): 2616-2629. doi: 10.1093/molbev/msaa113
[85]	Wang XG, Ju ZH, Jiang Q, Zhong JF, Liu CK, Wang JP, Hoff JL, Schnabel RD, Zhao H, Gao YP, Liu WH, Wang LL, Gao YD, Yang CH, Hou MH, Huang N, Regitano LCA, Porto-Neto LR, Decker JE, Taylor JF, Huang JM. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. Genomics, 2021, 113(3): 1491-1503. doi: 10.1016/j.ygeno.2021.03.023 pmid: 33771637
[86]	Liu KJ, Steinberg E, Yozzo A, Song Y, Kohn MH, Nakhleh L. Interspecific introgressive origin of genomic diversity in the house mouse. Proc Natl Acad Sci USA, 2015, 112(1): 196-201. doi: 10.1073/pnas.1406298111 pmid: 25512534
[87]	Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang XF, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science, 2015, 347(6217): 1258524. doi: 10.1126/science.1258524
[88]	Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol, 2018, 2(12): 1940-1955. doi: 10.1038/s41559-018-0717-x pmid: 30455444
[89]	Whitney KD, Broman KW, Kane NC, Hovick SM, Randell RA, Rieseberg LH. Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower. Mol Ecol, 2015, 24(9): 2194-2211. doi: 10.1111/mec.13044 pmid: 25522096
[90]	Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, Purugganan MD. The rice paradox: multiple origins but single domestication in asian rice. Mol Biol Evol, 2017, 34(4): 969-979. doi: 10.1093/molbev/msx049 pmid: 28087768
[91]	Merotto A, Goulart ICGR, Nunes AL, Kalsing A, Markus C, Menezes VG, Wander AE. Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in brazil. Evol Appl, 2016, 9(7): 837-846. doi: 10.1111/eva.12387 pmid: 27468302
[92]	Hoffmann AA, Miller AD, Weeks AR. Genetic mixing for population management: from genetic rescue to provenancing. Evol Appl, 2020, 14(3): 634-652. doi: 10.1111/eva.13154
[93]	Tricou T, Tannier E, De Vienne DM. Ghost lineages highly influence the interpretation of introgression tests. Syst Biol, 2022, 71(5): 1147-1158. doi: 10.1093/sysbio/syac011
[94]	Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biol, 2016, 14(12): e2000234. doi: 10.1371/journal.pbio.2000234
[95]	Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet, 2013, 9(2): e1003264. doi: 10.1371/journal.pgen.1003264
[96]	Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P. Multilocus approaches for the measurement of selection on correlated genetic loci. Mol Ecol, 2017, 26(1): 365-382. doi: 10.1111/mec.13867 pmid: 27696571

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统计量	检测策略	功能	计算原理
rIBD	遗传相似性	个体间的定性分析	个体间IBD相似性
χ²	遗传相似性	群体间的定性分析	群体间单倍型相似性
D	频率差异及拓扑结构分析	个体或群体间的定性分析	ABBA与BABA频率差异
f₄/f₄-ratio	频率差异及拓扑结构分析	群体间定性/定量分析	群体间等位基因频率差异的平均相关性
f_d	频率差异及拓扑结构分析	个体或群体间的滑窗定量分析	基于D统计量分子构建完全渗入模型
f_dM	频率差异及拓扑结构分析	个体或群体间的滑窗定量分析	在f_d基础上同等量化H₁、H₃和H₂、H₃之间的基因流
D_p	频率差异及拓扑结构分析	个体或群体间的定量分析	扩展D统计量分母包含全部位点模式

渗入方向	统计量
渗入方向	D_FO	D_IL	D_FI	D_OL
无	0	0	0	0
H₁→H₃	+	+	+	+
H₃→H₁	+	0	+	+
H₁→H₄	-	-	0	+
H₄→H₁	-	0	+	+
H₂→H₃	+	+	-	0
H₃→H₂	0	+	-	-
H₂→H₄	-	-	0	-
H₄→H₂	0	-	-	-
H₁₂→H₃	+	+	0	0
H₃→H₁₂	+	+	0	0
H₁₂→H₄	-	-	0	0
H₄→H₁₂	-	-	0	0
H_{1$\rightleftarrows $}H₂	0	0	0	0
H_{2$\rightleftarrows $}H₄	0	0	0	0

供体	受体	渗入位点	适应性特征	参考文献
丹尼索瓦人	藏族人	EPAS1	适应高原缺氧环境	[82]
丹尼索瓦人尼安德特人	现代人类	TLR10	先天免疫	[52]
黑尾兔	雪兔	ASIP	多态性季节伪装	[16]
阿尔及利亚小鼠	家鼠	Vkorc1	华法林杀鼠剂抗性	[86]
野山羊	现代山羊	MUC6	肠道病原体免疫	[5]
冈比亚按蚊群	-	常染色体中大量渗入	杀虫剂抗性	[87]
慈鲷鱼群	-	RH2B	深水适应性	[88]
Heliconius蝴蝶群	-	RAY	翅膀颜色图案	[22]
毛果杨	黑杨	PRR5 CMOT1	调节转录叶片氮含量	[6]
北美向日葵	向日葵	多个QTL	种子和花粉数量	[89]

基因渗入的检测和表征方法

Methods to detect and characterize introgression

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