Advances in lineage sorting theories and their detection methods

doi:10.17520/biods.2023400

Abstract

Abstract:

Background & Aims: Lineage sorting (LS) refers to the process in which multiple populations are descended from a common ancestral population or species and are now reproductively isolated from one another. It provides an approach to gain insights into speciation, and is often classified into the phases of polyphyly, paraphyly, and monophyly. The first two phases are in the state of incomplete lineage sorting (ILS) where gene trees do not correctly reflect species trees. The third phase is in the state of complete LS where gene trees are concordant with species trees. Here, we reviewed relevant theories and summarized recent progresses in method for LS detection.

Progress: We first systematically discussed the coalescent theories of how genome sites with distinct evolutionary properties (neutral or selective) in an ancestral population were transmitted to progeny populations. We discussed the potential relationships between gene trees and species trees for neutral and selective genes, respectively. Secondly, we delved into LS analyses based on the neutral DNA sequences, including construction of phylogeny under ILS and the network-based phylogenetic analysis. We then discussed the impacts of selection on LS analysis and methods for detecting both directional and balancing selection based on gene trees and species trees. Finally, we discussed a few open questions about the effects of mating system on LS, the detection of ILS, and the effects of pollen and seed flow on LS.

Prospect: New theories are needed to explore how mating system shapes the LS process for both selective and neutral genes. To appropriately assess ILS for individual genes based on species trees, it is crucial to improve the method estimating species trees and to fully utilize the potential of genome sequence data in future study. Given a high frequency of natural hybridization in plant species, a phylogenetic network method is needed to simultaneously examine pollen and seed flow together with ILS. Answers to these questions could help us to understand in-depth the LS process in plant species.

Key words: phylogeny, gene tree, species tree, gene flow, selection

Yanwen Lv, Ziyun Wang, Yu Xiao, Zihan He, Chao Wu, Xinsheng Hu. Advances in lineage sorting theories and their detection methods[J]. Biodiv Sci, 2024, 32(4): 23400.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2023400

https://www.biodiversity-science.net/EN/Y2024/V32/I4/23400

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References 193

[1]	Allman ES, Degnan JH, Rhodes JA (2018) Species tree inference from gene splits by unrooted STAR methods. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15, 337-342. DOI PMID
[2]	Avise JC, Shapira JF, Daniel SW, Aquadro CF, Lansman RA (1983) Mitochondrial DNA differentiation during the speciation process in Peromyscus. Molecular Biology and Evolution, 1, 38-56. PMID
[3]	Avni E, Cohen R, Snir S (2015) Weighted quartets phylogenetics. Systematic Biology, 64, 233-242. DOI PMID
[4]	Barluenga M, Austerlitz F, Elzinga JA, Teixeira S, Goudet J, Bernasconi G (2011) Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity, 106, 13-24. DOI PMID
[5]	Barton NH (1998) The effect of hitch-hiking on neutral genealogies. Genetics Research, 72, 123-133.
[6]	Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH (2007) Evolution. Cold Spring Harbor Laboratory Press, New York.
[7]	Barton NH, Etheridge AM, Sturm AK (2004) Coalescence in a random background. Annals of Applied Probability, 14, 754-785.
[8]	Bayzid MS, Hunt T, Warnow T (2014) Disk covering methods improve phylogenomic analyses. BMC Genomics, 15, S7.
[9]	Berbel-Filho WM, Pacheco G, Tatarenkov A, Lira MG, Garcia de Leaniz C, Rodríguez López CM, Lima SMQ, Consuegra S (2022) Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias. Molecular Phylogenetics and Evolution, 177, 107617.
[10]	Bitarello BD, De Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM (2018) Signatures of long-term balancing selection in human genomes. Genome Biology and Evolution, 10, 939-955. DOI PMID
[11]	Blair C, Ané C (2020) Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. Systematic Biology, 69, 593-601. DOI PMID
[12]	Bourret TB, Choudhury RA, Mehl HK, Blomquist CL, McRoberts N, Rizzo DM (2018) Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora. PLoS ONE, 13, e0192502.
[13]	Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29, 1917-1932. DOI PMID
[14]	Burbrink FT, Guiher TJ (2015) Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon. Zoological Journal of the Linnean Society, 173, 505-526.
[15]	Bustamante CD (2005) Population genetics of molecular evolution. In: Statistical Methods in Molecular Evolution (eds Mitchell H, Jonathan MS). Springer, New York.
[16]	Chan KO, Hutter CR, Wood PL Jr, Grismer LL, Das I, Brown RM (2020) Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Molecular Ecology, 29, 3970-3987.
[17]	Chapurlat E, Le Roncé I, Ågren J, Sletvold N (2020) Divergent selection on flowering phenology but not on floral morphology between two closely related orchids. Ecology and Evolution, 10, 5737-5747. DOI PMID
[18]	Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics, 134, 1289-1303. DOI PMID
[19]	Charlesworth D (2006) Balancing selection and its effects on sequences in nearby genome regions. PLoS Genetics, 2, e64.
[20]	Chen Q, Yang H, Feng X, Chen QJ, Shi SS, Wu CI, He ZW (2022) Two decades of suspect evidence for adaptive molecular evolution—Negative selection confounding positive-selection signals. National Science Review, 9, nwab217.
[21]	Cheng X, Li LL, Xiao Y, Chen XY, Hu XS (2020) Advances in the methods of detecting interspecific gene introgression and their applications. Scientia Sinica (Vitae), 50, 1388-1404. (in Chinese with English abstract)
	[程祥, 李玲玲, 肖钰, 陈晓阳, 胡新生 (2020) 种间基因渐渗检测方法及其应用研究进展. 中国科学: 生命科学, 50, 1388-1404.]
[22]	Cheng XH, DeGiorgio M (2019) Detection of shared balancing selection in the absence of trans-species polymorphism. Molecular Biology and Evolution, 36, 177-199. DOI PMID
[23]	Cheng XH, DeGiorgio M (2022) BalLeRMix+: Mixture model approaches for robust joint identification of both positive selection and long-term balancing selection. Bioinformatics, 38, 861-863.
[24]	Chifman J, Kubatko L (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics, 30, 3317-3324. DOI PMID
[25]	Chifman J, Kubatko L (2015) Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. Journal of Theoretical Biology, 374, 35-47. DOI PMID
[26]	Chung Y, Ané C (2011) Comparing two Bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer. Systematic Biology, 60, 261-275. DOI PMID
[27]	Cui RF, Schumer M, Kruesi K, Walter RB, Andolfatto P, Rosenthal GC (2013) Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution, 67, 2166-2179.
[28]	Cutter AD (2019) Reproductive transitions in plants and animals: Selfing syndrome, sexual selection and speciation. New Phytologist, 224, 1080-1094. DOI PMID
[29]	Dasarathy G, Nowak R, Roch S (2015) Data requirement for phylogenetic inference from multiple loci: A new distance method. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12, 422-432. DOI PMID
[30]	De Maio N, Schlötterer C, Kosiol C (2013) Linking great apes genome evolution across time scales using polymorphism- aware phylogenetic models. Molecular Biology and Evolution, 30, 2249-2262.
[31]	De Maio N, Schrempf D, Kosiol C (2015) PoMo: An allele frequency-based approach for species tree estimation. Systematic Biology, 64, 1018-1031. DOI PMID
[32]	DeGiorgio M, Lohmueller KE, Nielsen R (2014) A model-based approach for identifying signatures of ancient balancing selection in genetic data. PLoS Genetics, 10, e1004561.
[33]	Degnan JH (2018) Modeling hybridization under the network multispecies coalescent. Systematic Biology, 67, 786-799. DOI PMID
[34]	Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution, 24, 332-340.
[35]	Disanto F, Schlizio A, Wiehe T (2013) Yule-generated trees constrained by node imbalance. Mathematical Biosciences, 246, 139-147. DOI PMID
[36]	Duan L, Fu L, Chen HF (2023) Phylogenomic cytonuclear discordance and evolutionary histories of plants and animals. Science China: Life Sciences, 66, 2946-2948.
[37]	Dutheil JY, Munch K, Nam K, Mailund T, Schierup MH (2015) Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence. PLoS Genetics, 11, e1005451.
[38]	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, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J (2019) Genomic architecture and introgression shape a butterfly radiation. Science, 366, 594-599. DOI PMID
[39]	Elworth RAL, Ogilvie HA, Zhu J, Nakhleh L (2019) Advances in computational methods for phylogenetic networks in the presence of hybridization. In: Bioinformatics and Phylogenetics (ed. Warnow T). Springer, Cham.
[40]	Eyre-Walker A, Keightley PD (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Molecular Biology and Evolution, 26, 2097-2108. DOI PMID
[41]	Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics, 155, 1405-1413. DOI PMID
[42]	Ferretti L, Ledda A, Wiehe T, Achaz G, Ramos-Onsins SE (2017) Decomposing the site frequency spectrum: The impact of tree topology on neutrality tests. Genetics, 207, 229-240. DOI PMID
[43]	Firneno TJ Jr, O’Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK (2020) Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Molecular Ecology, 29, 3543-3559.
[44]	Fisher RA (1930) The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
[45]	Flouri T, Jiao XY, Rannala B, Yang ZH (2020) A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Molecular Biology and Evolution, 37, 1211-1223. DOI PMID
[46]	Forsythe ES, Nelson ADL, Beilstein MA (2020) Biased gene retention in the face of introgression obscures species relationships. Genome Biology and Evolution, 12, 1646-1663. DOI PMID
[47]	Galtier N (2016) Adaptive protein evolution in animals and the effective population size hypothesis. PLoS Genetics, 12, e1005774.
[48]	Gao ZY, Przeworski M, Sella G (2015) Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species. Evolution, 69, 431-446. DOI PMID
[49]	Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, Harrison RD, Hipp AL, Holvoet M, Khew G, Kjellberg F, Liao S, Pederneiras LC, Peng YQ, Pereira JT, Phillipps Q, Ahmad Puad AS, Rasplus JY, Sang J, Schou SJ, Velautham E, Weiblen GD, Zerega NJC, Zhang Q, Zhang Z, Baraloto C, Rønsted N (2023) Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs. Proceedings of the National Academy of Sciences, USA, 120, e2222035120.
[50]	Gatesy J, Springer MS (2014) Phylogenetic analysis at deep timescales:Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Molecular Phylogenetics and Evolution, 80, 231-266.
[51]	Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ (2023) Phylogenomics and the flowering plant tree of life. Journal of Integrative Plant Biology, 65, 299-323. DOI
[52]	Gussow AB, Petrovski S, Wang QL, Allen AS, Goldstein DB (2016) The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. Genome Biology, 17, 9.
[53]	Haldane JBS (1927) A mathematical theory of natural and artificial selection, part V: Selection and mutation. Mathematical Proceedings of the Cambridge Philosophical Society, 23, 838-844.
[54]	Han YH, Molloy EK (2023) Improving quartet graph construction for scalable and accurate species tree estimation from gene trees. Genome Research, 33, 1042-1052. DOI PMID
[55]	Harris RB, Jensen JD (2020) Considering genomic scans for selection as coalescent model choice. Genome Biology and Evolution, 12, 871-877. DOI PMID
[56]	Hayeck TJ, Stong N, Wolock CJ, Copeland B, Kamalakaran S, Goldstein DB, Allen AS (2019) Improved pathogenic variant localization via a hierarchical model of sub-regional intolerance. The American Journal of Human Genetics, 104, 299-309.
[57]	He B, Zhao YJ, Su CY, Lin GH, Wang YL, Li LY, Ma JY, Yang Q, Hao JS (2023) Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius). Systematic Entomology, 48, 585-599.
[58]	Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580. DOI PMID
[59]	Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff SA, Sousa VC, Wang Y (2018) Phylogeny estimation by integration over isolation with migration models. Molecular Biology and Evolution, 35, 2805-2818. DOI PMID
[60]	Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
[61]	Hey J, Nielsen R (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA, 104, 2785-2790.
[62]	Hill M, Legried B, Roch S (2022) Species tree estimation under joint modeling of coalescence and duplication: Sample complexity of quartet methods. Annals of Applied Probability, 32, 4681-4705.
[63]	Hu XS (2015) Mating system as a barrier to gene flow. Evolution, 69, 1158-1177.
[64]	Hu XS, Ennos RA (1997) On estimation of the ratio of pollen to seed flow among plant populations. Heredity, 79, 541-552.
[65]	Hu Y, Wang X, Zhang XX, Zhou W, Chen XY, Hu XS (2019) Advancing phylogeography with chloroplast DNA markers. Biodiversity Science, 27, 219-234. (in Chinese with English abstract) DOI
	[胡颖, 王茜, 张新新, 周玮, 陈晓阳, 胡新生 (2019) 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, 27, 219-234.] DOI
[66]	Hudson RR, Kaplan NL (1988) The coalescent process in models with selection and recombination. Genetics, 120, 831-840. DOI PMID
[67]	Hudson RR, Kaplan NL (1995a) The coalescent process and background selection. Philosophical Transactions of the Royal Society B: Biological Sciences, 349, 19-23.
[68]	Hudson RR, Kaplan NL (1995b) Deleterious background selection with recombination. Genetics, 141, 1605-1617.
[69]	Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153-159. DOI PMID
[70]	Hunter-Zinck H, Clark AG (2015) Aberrant time to most recent common ancestor as a signature of natural selection. Molecular Biology and Evolution, 32, 2784-2797. DOI PMID
[71]	Isildak U, Stella A, Fumagalli M (2021) Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. Molecular Ecology Resources, 21, 2706-2718.
[72]	Islam M, Sarker K, Das T, Reaz R, Bayzid MS (2020) STELAR: A statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. BMC Genomics, 21, 136. DOI PMID
[73]	Jiang XD, Edwards SV, Liu L (2020) The multispecies coalescent model outperforms concatenation across diverse phylogenomic data sets. Systematic Biology, 69, 795-812. DOI PMID
[74]	Joffard N, Le Roncé I, Langlois A, Renoult J, Buatois B, Dormont L, Schatz B (2020) Floral trait differentiation in Anacamptis coriophora: Phenotypic selection on scents, but not on colour. Journal of Evolutionary Biology, 33, 1028-1038.
[75]	Johnson KE, Voight BF (2018) Patterns of shared signatures of recent positive selection across human populations. Nature Ecology & Evolution, 2, 713-720.
[76]	Jones G, Sagitov S, Oxelman B (2013) Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology, 62, 467-478. DOI PMID
[77]	Kamneva OK, Syring J, Liston A, Rosenberg NA (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evolutionary Biology, 17, 180. DOI PMID
[78]	Kao TT, Wang TH, Ku C (2022) Rampant nuclear- mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae. New Phytologist, 235, 1394-1408.
[79]	Kaplan N, Hudson RR, Iizuka M (1991) The coalescent process in models with selection, recombination and geographic subdivision. Genetics Research, 57, 83-91. PMID
[80]	Kaplan NL, Darden T, Hudson RR (1988) The coalescent process in models with selection. Genetics, 120, 819-829. DOI PMID
[81]	Kelly JK, Wade MJ (2000) Molecular evolution near a two-locus balanced polymorphism. Journal of Theoretical Biology, 204, 83-101. PMID
[82]	Kimura M (1954) Process leading to quasi-fixation of genes in natural populations due to random fluctuation of selection intensities. Genetics, 39, 280-295. DOI PMID
[83]	Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics, 47, 713-719. PMID
[84]	Kingman JFC (1982) The coalescent. Stochastic Processes and Their Applications, 13, 235-248.
[85]	Klein J (1987) The major histocompatibility complex and protein recognition by T lymphocytes. In: Immunobiology of Proteins and Peptides IV: Advances in Experimental Medicine and Biology (ed. Atassi MZ), Springer, Boston, MA.
[86]	Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, Hughes CE (2020) Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytologist, 225, 1355-1369. DOI PMID
[87]	Kubatko LS, Carstens BC, Knowles LL (2009) STEM: Species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics, 25, 971-973. DOI PMID
[88]	Leaché AD, Harris RB, Rannala B, Yang ZH (2014) The influence of gene flow on species tree estimation: A simulation study. Systematic Biology, 63, 17-30. DOI PMID
[89]	Li F, Rane RV, Luria V, Xiong ZJ, Chen JW, Li ZM, Catullo RA, Griffin PC, Schiffer M, Pearce S, Lee SF, McElroy K, Stocker A, Shirriffs J, Cockerell F, Coppin C, Sgrò CM, Karger A, Cain JW, Weber JA, Santpere G, Kirschner MW, Hoffmann AA, Oakeshott JG, Zhang GJ (2022) Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Molecular Ecology Resources, 22, 1559-1581.
[90]	Li HP, Wiehe T (2013) Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Computational Biology, 9, e1003060.
[91]	Li LL, Wang X, Xiao Y, Cheng X, Chen XY, Hu XS (2023) On the theories of plant mating system and molecular evolution and their applications. Science China (Vitae), 53, 50-63. (in Chinese with English abstract )
	[李玲玲, 王茜, 肖钰, 程祥, 陈晓阳, 胡新生 (2023) 植物交配系统与分子进化理论及其应用研究. 中国科学: 生命科学, 53, 50-63.]
[92]	Li LL, Xiao Y, Wang X, He ZH, Lv YW, Hu XS (2023) The Ka/Ks and πa/πs ratios under different models of gametophytic and sporophytic selection. Genome Biology and Evolution, 15, evad151.
[93]	Liang M, Nielsen R (2014) The lengths of admixture tracts. Genetics, 197, 953-967. DOI PMID
[94]	Liu BQ, Warnow T (2023) Weighted ASTRID: Fast and accurate species trees from weighted internode distances. Algorithms for Molecular Biology, 18, 6. DOI PMID
[95]	Liu L (2008) BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics, 24, 2542-2543. DOI PMID
[96]	Liu L, Yu L (2011) Estimating species trees from unrooted gene trees. Systematic Biology, 60, 661-667. DOI PMID
[97]	Liu L, Yu L, Edwards SV (2010) A maximum pseudo- likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology, 10, 302.
[98]	Liu L, Yu L, Pearl DK, Edwards SV (2009) Estimating species phylogenies using coalescence times among sequences. Systematic Biology, 58, 468-477. DOI PMID
[99]	Liu L, Yu LL (2010) Phybase: An R package for species tree analysis. Bioinformatics, 26, 962-963. DOI PMID
[100]	Long C, Kubatko L (2018) The effect of gene flow on coalescent-based species-tree inference. Systematic Biology, 67, 770-785. DOI PMID
[101]	Mahbub M, Wahab Z, Reaz R, Rahman MS, Bayzid MS (2021) wQFM: Highly accurate genome-scale species tree estimation from weighted quartets. Bioinformatics, 37, 3734-3743. DOI PMID
[102]	Mailund T, Munch K, Schierup MH (2014) Lineage sorting in apes. Annual Review of Genetics, 48, 519-535. DOI PMID
[103]	Mallet J, Besansky N, Hahn MW (2016) How reticulated are species? BioEssays, 38, 140-149. DOI PMID
[104]	Mao Y, Economo EP, Satoh N (2018) The roles of introgression and climate change in the rise to dominance of Acropora corals. Current Biology, 28, 3373-3382.
[105]	Mao Y, Hou S, Shi J, Economo EP (2020) TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data. Molecular Ecology Resources, 20, 832-840.
[106]	Markin A, Eulenstein O (2021) Quartet-based inference is statistically consistent under the unified duplication-loss- coalescence model. Bioinformatics, 37, 4064-4074.
[107]	Messer PW, Petrov DA (2013) Frequent adaptation and the McDonald-Kreitman test. Proceedings of the National Academy of Sciences, USA, 110, 8615-8620.
[108]	Mirarab S, Nakhleh L, Warnow T (2021) Multispecies coalescent: Theory and applications in phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 52, 247-268.
[109]	Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T (2014) ASTRAL: Genome-scale coalescent- based species tree estimation. Bioinformatics, 30, 541-548. DOI PMID
[110]	Mirarab S, Warnow T (2015) ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31, 44-52. DOI PMID
[111]	Moghe GD, Shiu SH (2014) The causes and molecular consequences of polyploidy in flowering plants. Annals of the New York Academy of Sciences, 1320, 16-34.
[112]	Molloy EK, Warnow T (2018) To include or not to include: The impact of gene filtering on species tree estimation methods. Systematic Biology, 67, 285-303. DOI PMID
[113]	Moran PAP (1958) Random processes in genetics. Mathematical Proceedings of the Cambridge Philosophical Society, 54, 60-71.
[114]	Moran PAP (1962) The Statistical Processes of Evolutionary Theory. Clarendon Press, Oxford.
[115]	Morel B, Williams TA, Stamatakis A (2023) Asteroid: A new algorithm to infer species trees from gene trees under high proportions of missing data. Bioinformatics, 39, btac832.
[116]	Munch K, Nam K, Schierup MH, Mailund T (2016) Selective sweeps across twenty million years of primate evolution. Molecular Biology and Evolution, 33, 3065-3074.
[117]	Murga-Moreno J, Coronado-Zamora M, Casillas S, Barbadilla A (2022) impMKT: The imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level. G3: Genes\|Genomes\|Genetics, 12, jkac206.
[118]	Neuhauser C, Krone SM (1997) The genealogy of samples in models with selection. Genetics, 145, 519-534. DOI PMID
[119]	Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A (2018) Speciation generates mosaic genomes in kangaroos. Genome Biology and Evolution, 10, 33-44. DOI PMID
[120]	Nute M, Chou J, Molloy EK, Warnow T (2018) The performance of coalescent-based species tree estimation methods under models of missing data. BMC Genomics, 19, 286. DOI PMID
[121]	Ogilvie HA, Bouckaert RR, Drummond AJ (2017) StarBEAST 2 brings faster species tree inference and accurate estimates of substitution rates. Molecular Biology and Evolution, 34, 2101-2114. DOI PMID
[122]	Olave M, Meyer A (2020) Implementing large genomic single nucleotide polymorphism data sets in phylogenetic network reconstructions: A case study of particularly rapid radiations of cichlid fish. Systematic Biology, 69, 848-862. DOI PMID
[123]	Palamara PF, Terhorst J, Song YS, Price AL (2018) High- throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nature Genetics, 50, 1311-1317.
[124]	Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Molecular Biology and Evolution, 5, 568-83. DOI PMID
[125]	Patwa Z, Wahl LM (2008) The fixation probability of beneficial mutations. Journal of the Royal Society, 5, 1279-1289.
[126]	Pei JW, Wu YF (2017) STELLS2: Fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies. Bioinformatics, 33, 1789-1797. DOI PMID
[127]	Poh YP, Domingues VS, Hoekstra HE, Jensen JD (2014) On the prospect of identifying adaptive loci in recently bottlenecked populations. PLoS ONE, 9, e110579.
[128]	Pollard DA, Iyer VN, Moses AM, Eisen MB (2006) Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting. PLoS Genetics, 2, e173.
[129]	Poroshina AA, Sherbakov DY, Peretolchina TE (2020) Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers. Vavilov Journal of Genetics and Breeding, 24, 420-426.
[130]	Przeworski M, Charlesworth B, Wall JD (1999) Genealogies and weak purifying selection. Molecular Biology and Evolution, 16, 246-252. PMID
[131]	Rannala B, Yang ZH (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656. DOI PMID
[132]	Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology, 66, 857-879. DOI PMID
[133]	Rendón-Anaya M, Ibarra-Laclette E, Méndez-Bravo A, Lan T, Zheng C, Carretero-Paulet L, Perez-Torres CA, Chacón- López A, Hernandez-Guzmán G, Chang TH, Farr KM, Barbazuk WB, Chamala S, Mutwil M, Shivhare D, Alvarez- Ponce D, Mitter N, Hayward A, Fletcher S, Rozas J, Sánchez Gracia A, Kuhn D, Barrientos-Priego AF, Salojärvi J, Librado P, Sankoff D, Herrera-Estrella A, Albert VA, Herrera-Estrella L (2019) The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proceedings of the National Academy of Sciences, USA, 116, 17081-17089.
[134]	Rhodes JA, Nute MG, Warnow T (2020) NJst and ASTRID are not statistically consistent under a random model of missing data. ArXiv, doi: 10.48550/arXiv.2001.07844.
[135]	Richards A, Kubatko L (2021) Bayesian-weighted triplet and quartet methods for species tree inference. Bulletin of Mathematical Biology, 83, 93. DOI PMID
[136]	Rifkin JL, Castillo AS, Liao IT, Rausher MD (2019) Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Molecular Ecology, 28, 1709-1729. DOI PMID
[137]	Roch S, Steel M (2015) Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theoretical Population Biology, 100, 56-62.
[138]	Sackton TB, Clark N (2019) Convergent evolution in the genomics era: New insights and directions. Philosophical Transactions of the Royal Society B: Biological Sciences, 374, 20190102.
[139]	Santos SHD, Peery RM, Miller JM, Dao A, Lyu FH, Li X, Li MH, Coltman DW (2021) Ancient hybridization patterns between bighorn and thinhorn sheep. Molecular Ecology, 30, 6273-6288. DOI PMID
[140]	Sarver BAJ, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM (2017) Phylogenomic insights into mouse evolution using a pseudoreference approach. Genome Biology and Evolution, 9, 726-739. DOI PMID
[141]	Sawyer SA, Hartl DL (1992) Population genetics of polymorphism and divergence. Genetics, 132, 1161-1176. DOI PMID
[142]	Sayyari E, Mirarab S (2016) Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. BMC Genomics, 17, 783. DOI PMID
[143]	Sheehan S, Song YS (2016) Deep learning for population genetic inference. Genome Biology and Evolution, 15, e1004845.
[144]	Shi CM, Yang ZH (2018) Coalescent-based analyses of genomic sequence data provide a robust resolution of phylogenetic relationships among major groups of gibbons. Molecular Biology and Evolution, 35, 159-179.
[145]	Siewert KM, Voight BF (2017) Detecting long-term balancing selection using allele frequency correlation. Molecular Biology and Evolution, 34, 2996-3005. DOI PMID
[146]	Slade PF (2000) Most recent common ancestor probability distributions in gene genealogies under selection. Theoretical Population Biology, 58, 291-305. PMID
[147]	Smith JM, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genetical Research, 23, 23-35.
[148]	Solís-Lemus C, Ané C (2016) Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12, e1005896.
[149]	Solís-Lemus C, Bastide P, Ané C (2017) PhyloNetworks: A package for phylogenetic networks. Molecular Biology and Evolution, 34, 3292-3298. DOI PMID
[150]	Soltis PS, Marchant DB, Van De Peer Y, Soltis DE (2015) Polyploidy and genome evolution in plants. Current Opinion in Genetics & Development, 35, 119-125.
[151]	Song S, Liu L, Edwards SV, Wu S (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proceedings of the National Academy of Sciences, USA, 109, 14942-14947.
[152]	Stephens M, Donnelly P (2003) Ancestral inference in population genetics models with selection (with discussion). Australian & New Zealand Journal of Statistics, 45, 395-430.
[153]	Stull GW, Pham KK, Soltis PS, Soltis DE (2023) Deep reticulation: The long legacy of hybridization in vascular plant evolution. The Plant Journal, 114, 743-766. DOI PMID
[154]	Sukumaran J, Holder MT (2010) DendroPy: A Python library for phylogenetic computing. Bioinformatics, 26, 1569-1571. DOI PMID
[155]	Tabatabaee Y, Roch S, Warnow T (2023) Statistically consistent rooting of species trees under the multispecies coalescent model. In: Research in Computational Molecular Biology (ed. Tang H). Springer, Cham.
[156]	Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460. DOI PMID
[157]	Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595. DOI PMID
[158]	Takahata N, Nei M (1990) Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics, 124, 967-978. DOI PMID
[159]	Thornton KR, Jensen JD (2007) Controlling the false-positive rate in multilocus genome scans for selection. Genetics, 175, 737-750. PMID
[160]	To TH, Scornavacca C (2015) Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. BMC Genomics, 16, S6.
[161]	Vachaspati P, Warnow T (2015) ASTRID: Accurate species TRees from internode distances. BMC Genomics, 16, S3.
[162]	Vachaspati P, Warnow T (2018) SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution, 124, 122-136. DOI PMID
[163]	Wakeley J (2008) Conditional gene genealogies under strong purifying selection. Molecular Biology and Evolution, 25, 2615-2626. DOI PMID
[164]	Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM (2012) The structure of genealogies in the presence of purifying selection: A fitness-class coalescent. Genetics, 190, 753-779. DOI PMID
[165]	Wang MX, Huang X, Li R, Xu HY, Jin L, He YG (2014) Detecting recent positive selection with high accuracy and reliability by conditional coalescent tree. Molecular Biology and Evolution, 31, 3068-3080. DOI PMID
[166]	Wang X, Cheng X, Zhou W, Zhang XX, Hu Y, Chen XY, Hu XS (2019) Assessing the ecological and evolutionary processes underlying cytonuclear interactions. Scientia Sinica (Vitae), 49, 951-964. (in Chinese with English abstract)
	[王茜, 程祥, 周玮, 张新新, 胡颖, 陈晓阳, 胡新生 (2019) 细胞核质互作形成的生态与进化过程分析. 中国科学: 生命科学, 49, 951-964.]
[167]	Wang X, Xiao Y, He ZH, Li LL, Song HY, Zhang JJ, Cheng X, Chen XY, Li P, Hu XS (2022) A chromosome-level genome assembly of Toona ciliata (Meliaceae). Genome Biology and Evolution, 14, evac121.
[168]	Wang Y, Hey J (2010) Estimating divergence parameters with small samples from a large number of loci. Genetics, 184, 363-379. DOI PMID
[169]	Wascher M, Kubatko L (2021) Consistency of SVDQuartets and maximum likelihood for coalescent-based species tree estimation. Systematic Biology, 70, 33-48. DOI PMID
[170]	Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276. DOI PMID
[171]	Wen D, Nakhleh L (2018) Coestimating reticulate phylogenies and gene trees from multilocus sequence data. Systematic Biology, 67, 439-457. DOI PMID
[172]	Wen D, Yu Y, Zhu J, Nakhleh L (2018) Inferring phylogenetic networks using PhyloNet. Systematic Biology, 67, 735-740. DOI PMID
[173]	Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M (2011) A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genetics, 7, e1002395.
[174]	Wright S (1942) Statistical genetics and evolution. Bulletin of the American Mathematical Society, 48, 223-246.
[175]	Wu Y (2012) Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution, 66, 763-775. DOI PMID
[176]	Xi ZX, Liu L, Rest JS, Davis CC (2014) Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Systematic Biology, 63, 919-932.
[177]	Xiao Y, Wang X, He ZH, Li LL, Hu XS (2022) Advances in speciation theories and their verifications based on the biological species concept. Biodiversity Science, 30, 21480. (in Chinese with English abstract) DOI
	[肖钰, 王茜, 何梓晗, 李玲玲, 胡新生 (2022) 基于生物学物种定义探讨物种形成理论与验证的研究进展. 生物多样性, 30, 21480.] DOI
[178]	Xu L, Yu R, Lin X, Zhang BW, Li N, Lin K, Zhang DY, Bai WN (2021) Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. New Phytologist, 232, 388-403. DOI PMID
[179]	Yan Z, Cao Z, Liu YS, Ogilvie HA, Nakhleh L (2022) Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes. Systematic Biology, 71, 706-720.
[180]	Yang ZF, Li JR, Wiehe T, Li HP (2018) Detecting recent positive selection with a single locus test bipartitioning the coalescent tree. Genetics, 208, 791-805. DOI PMID
[181]	Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586-1591. DOI PMID
[182]	Yang ZH (2015) The BPP program for species tree estimation and species delimitation. Current Zoology, 61, 854-865.
[183]	Yu Y, Degnan JH, Nakhleh L (2012) The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics, 8, e1002660.
[184]	Yu Y, Dong JR, Liu KJ, Nakhleh L (2014) Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences, USA, 111, 16448-16453.
[185]	Yu Y, Nakhleh L (2015) A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genomics, 16, S10.
[186]	Zhang C, Mirarab S (2022) Weighting by gene tree uncertainty improves accuracy of quartet-based species trees. Molecular Biology and Evolution, 39, msac215.
[187]	Zhang C, Ogilvie HA, Drummond AJ, Stadler T (2018a) Bayesian inference of species networks from multilocus sequence data. Molecular Biology and Evolution, 35, 504-517.
[188]	Zhang C, Rabiee M, Sayyari E, Mirarab S (2018b) ASTRAL- III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19, 153.
[189]	Zhou BF, Yuan S, Crowl AA, Liang YY, Shi Y, Chen XY, An QQ, Kang M, Manos PS, Wang BS (2022) Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nature Communications, 13, 1320.
[190]	Zhu JF, Nakhleh L (2018) Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. Bioinformatics, 34, 376-385. DOI PMID
[191]	Zhu JF, Wen DQ, Yu Y, Meudt HM, Nakhleh L (2018) Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLoS Computational Biology, 14, e1005932.
[192]	Zimmermann T, Mirarab S, Warnow T (2014) BBCA: Improving the scalability of *BEAST using random binning. BMC Genomics, 15, S11.
[193]	Zou XH, Ge S (2008) Conflicting gene trees and phylogenomics. Journal of Systematics and Evolution, 46, 795-807. (in Chinese with English abstract)
	[邹新慧, 葛颂 (2008) 基因树冲突与系统发育基因组学研究. 植物分类学报, 46, 795-807.]

祖先群体中选择类型 Selection type at a locus in the ancestral population	子代物种间基因平均溯祖时间 Mean coalescent time between orthologous genes from descent species
定向选择 Directional selection	近似于在祖先群体时溯祖时间, 或长于物种分化时间 Approximate to the coalescent time in the ancestral population, or longer than the species divergence time
平衡选择 Balancing selection	远远大于物种分化时间 Much longer than the species divergence time
歧化选择 Disruptive selection	近似于物种分化时间 Approximate to the species divergence time
正频率依赖选择 Positive frequency-dependent selection	近似于在祖先群体时的溯祖时间 Approximate to the coalescent time in the ancestral population
负频率依赖选择 Negative frequency-dependent selection	远远大于物种分化时间 Much longer than the species divergence time
随机选择 Stochastic selection	近似于子代物种中性基因间溯祖时间, 大于物种分化时间 Approximate to the coalescent time of neutral genes in decent species but is longer than the species divergence time

祖先群体中选择类型 Selection type at a locus in the ancestral population	子代物种间基因平均溯祖时间 Mean coalescent time between orthologous genes from descent species
定向选择 Directional selection	近似于在祖先群体时溯祖时间, 或长于物种分化时间 Approximate to the coalescent time in the ancestral population, or longer than the species divergence time
平衡选择 Balancing selection	远远大于物种分化时间 Much longer than the species divergence time
歧化选择 Disruptive selection	近似于物种分化时间 Approximate to the species divergence time
正频率依赖选择 Positive frequency-dependent selection	近似于在祖先群体时的溯祖时间 Approximate to the coalescent time in the ancestral population
负频率依赖选择 Negative frequency-dependent selection	远远大于物种分化时间 Much longer than the species divergence time
随机选择 Stochastic selection	近似于子代物种中性基因间溯祖时间, 大于物种分化时间 Approximate to the coalescent time of neutral genes in decent species but is longer than the species divergence time

类型 Type	输入/输出 Input/output	方法 Method	参考文献 References
汇总法 Summary method	无根基因树/无根物种树 UGT/UST	NJst	Liu & Yu, 2011
	无根基因树/无根物种树 UGT/UST	wQMC	Avni et al, 2015
	无根基因树/无根物种树 UGT/UST	ASTRAL	Mirarab et al, 2014
	无根基因树/无根物种树 UGT/UST	ASTRAL-II	Mirarab & Warnow, 2015
	无根基因树/无根物种树 UGT/UST	ASTRID	Vachaspati & Warnow, 2015
	无根基因树/无根物种树 UGT/UST	DISTIQUE	Sayyari & Mirarab, 2016
	无根基因树/无根物种树 UGT/UST	ASTRAL-III	Zhang et al, 2018b
	无根基因树/无根物种树 UGT/UST	USTAR/FastME	Allman et al, 2018
	无根基因树/无根物种树 UGT/UST	wQFM	Mahbub et al, 2021
	无根基因树/无根物种树 UGT/UST	ASTER	Zhang & Mirarab, 2022
	无根基因树/无根物种树 UGT/UST	TREE-QMC	Han & Molloy, 2023
	无根基因树/无根物种树 UGT/UST	Asteroid	Morel et al, 2023
	无根基因树/无根物种树 UGT/UST	wASTRID	Liu & Warnow, 2023
	有根基因树/有根物种树 RGT/RST	STEM	Kubatko et al, 2009
	有根基因树/有根物种树 RGT/RST	STAR/STEAC	Liu et al, 2009
	有根基因树/有根物种树 RGT/RST	MP-EST	Liu et al, 2010
	有根基因树/有根物种树 RGT/RST	STELLS	Wu, 2012
	有根基因树/有根物种树 RGT/RST	METAL	Dasarathy et al, 2015
	有根基因树/有根物种树 RGT/RST	STELLS2	Pei & Wu, 2017
	有根基因树/有根物种树 RGT/RST	QR-STAR	Tabatabaee et al, 2023
	有根基因树/无根物种树 RGT/UST	STELAR	Islam et al, 2020
共同估计法 Co-estimation of gene and species trees	多序列比对/有根物种树和基因树分布 MSA/DRSGT	BEST	Liu, 2008
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	*BEAST	Heled & Drummond, 2010
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	SNAP	Bryant et al, 2012
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	BPP	Yang, 2015
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	StarBEAST2	Ogilvie et al, 2017
基于位点法 Site-based method	多位点比对/无根物种树 Multi-site alignments/UST	SVDquartets	Chifman & Kubatko, 2015
	多位点比对/无根物种树 Multi-site alignments/UST	SVDquest	Vachaspati & Warnow, 2018
	独立溯祖位点/有根物种树 ICS/RST	Lily	Richards & Kubatko, 2021

类型 Type	输入/输出 Input/output	方法 Method	参考文献 References
汇总法 Summary method	无根基因树/无根物种树 UGT/UST	NJst	Liu & Yu, 2011
	无根基因树/无根物种树 UGT/UST	wQMC	Avni et al, 2015
	无根基因树/无根物种树 UGT/UST	ASTRAL	Mirarab et al, 2014
	无根基因树/无根物种树 UGT/UST	ASTRAL-II	Mirarab & Warnow, 2015
	无根基因树/无根物种树 UGT/UST	ASTRID	Vachaspati & Warnow, 2015
	无根基因树/无根物种树 UGT/UST	DISTIQUE	Sayyari & Mirarab, 2016
	无根基因树/无根物种树 UGT/UST	ASTRAL-III	Zhang et al, 2018b
	无根基因树/无根物种树 UGT/UST	USTAR/FastME	Allman et al, 2018
	无根基因树/无根物种树 UGT/UST	wQFM	Mahbub et al, 2021
	无根基因树/无根物种树 UGT/UST	ASTER	Zhang & Mirarab, 2022
	无根基因树/无根物种树 UGT/UST	TREE-QMC	Han & Molloy, 2023
	无根基因树/无根物种树 UGT/UST	Asteroid	Morel et al, 2023
	无根基因树/无根物种树 UGT/UST	wASTRID	Liu & Warnow, 2023
	有根基因树/有根物种树 RGT/RST	STEM	Kubatko et al, 2009
	有根基因树/有根物种树 RGT/RST	STAR/STEAC	Liu et al, 2009
	有根基因树/有根物种树 RGT/RST	MP-EST	Liu et al, 2010
	有根基因树/有根物种树 RGT/RST	STELLS	Wu, 2012
	有根基因树/有根物种树 RGT/RST	METAL	Dasarathy et al, 2015
	有根基因树/有根物种树 RGT/RST	STELLS2	Pei & Wu, 2017
	有根基因树/有根物种树 RGT/RST	QR-STAR	Tabatabaee et al, 2023
	有根基因树/无根物种树 RGT/UST	STELAR	Islam et al, 2020
共同估计法 Co-estimation of gene and species trees	多序列比对/有根物种树和基因树分布 MSA/DRSGT	BEST	Liu, 2008
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	*BEAST	Heled & Drummond, 2010
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	SNAP	Bryant et al, 2012
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	BPP	Yang, 2015
	多序列比对/有根物种树和基因树分布 MSA/DRSGT	StarBEAST2	Ogilvie et al, 2017
基于位点法 Site-based method	多位点比对/无根物种树 Multi-site alignments/UST	SVDquartets	Chifman & Kubatko, 2015
	多位点比对/无根物种树 Multi-site alignments/UST	SVDquest	Vachaspati & Warnow, 2018
	独立溯祖位点/有根物种树 ICS/RST	Lily	Richards & Kubatko, 2021