[1]

Finarelli JA, Flynn JJ. 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Systematic Biology 55:301−13

doi: 10.1080/10635150500541698
[2]

Schäffer S, Koblmüller S, Pfingstl T, Sturmbauer C, Krisper G. 2010. Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the 'Higher Oribatida' (Acari), conflicting with current classification schemes. BMC Evolutionary Biology 10:246−62

doi: 10.1186/1471-2148-10-246
[3]

Nürk NM, Madriñán S, Carine MA, Chase MW, Blattner FR. 2013. Molecular phylogenetics and morphological evolution of St. John's wort (Hypericum; Hypericaceae). Molecular Phylogenetics and Evolution 66:1−16

doi: 10.1016/j.ympev.2012.08.022
[4]

Sanger F, Thompson EOP, Kitai R. 1955. The amide groups of insulin. Biochemical Journal 59:509

doi: 10.1042/bj0590509
[5]

Pauling L, Zuckerkandl E, Henriksen T, Lövstad R. 1963. Chemical paleogenetics. Molecular 'restoration studies' of extinct forms of life. Acta Chemica Scandinavica 17:9−16

doi: 10.3891/acta.chem.scand.17s-0009
[6]

Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AFY. 2016. Ancestral reconstruction. PLoS Computational Biology 12:e1004763

doi: 10.1371/journal.pcbi.1004763
[7]

Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, et al. 2009. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 58:224−39

doi: 10.1093/sysbio/syp020
[8]

Caboň M, Eberhardt U, Looney B, Hampe F, Kolařík M, et al. 2017. New insights in Russula subsect. Rubrinae: phylogeny and the quest for synapomorphic characters. Mycological Progress 16:877−92

doi: 10.1007/s11557-017-1322-0
[9]

Yang DD, de Billerbeck GM, Zhang JJ, Rosenzweig F, Francois JM. 2017. Deciphering the origin, evolution, and physiological function of the subtelomeric aryl-alcohol dehydrogenase gene family in the yeast Saccharomyces cerevisiae. Applied and Environmental Microbiology 84:e01553-17

doi: 10.1128/AEM.01553-17
[10]

Wang XW, Varga T, Li QS, Nagy LG, Zhou LW. 2025. Complex evolutionary history of the fungal order Hymenochaetales revealed by analyses of trait evolution and diversification. Mycosphere 16:517−35

doi: 10.5943/mycosphere/16/1/7
[11]

Cunningham CW, Omland KE, Oakley TH. 1998. Reconstructing ancestral character states: a critical reappraisal. Trends in Ecology & Evolution 13:361−66

doi: 10.1016/S0169-5347(98)01382-2
[12]

Pagel M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48:612−22

doi: 10.1080/106351599260184
[13]

Divakar PK, Kauff F, Crespo A, Leavitt SD, Lumbsch HT. 2013. Understanding phenotypical character evolution in parmelioid lichenized fungi (Parmeliaceae, Ascomycota). PLoS One 8:e83115

doi: 10.1371/journal.pone.0083115
[14]

Soltis DE, Mort ME, Latvis M, Mavrodiev EV, Brian C O'Meara BC, et al. 2013. Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. American Journal of Botany 100:916−29

doi: 10.3732/ajb.1300044
[15]

Banks H, Forest F, Lewis G. 2014. Evolution and diversity of pollen morphology in tribe Cercideae (Leguminosae). TAXON 63:299−314

doi: 10.12705/632.37
[16]

Horn JW, Fisher JB, Tomlinson PB, Lewis CE, Laubengayer K. 2009. Evolution of lamina anatomy in the palm family (Arecaceae). American Journal of Botany 96:1462−86

doi: 10.3732/ajb.0800396
[17]

Givnish TJ, Pires JC, Graham SW, McPherson MA, Prince LM, et al. 2005. Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny. Proceedings Biological Sciences 272:1481−90

doi: 10.1098/rspb.2005.3067
[18]

Ricklefs RE. 2007. Estimating diversification rates from phylogenetic information. Trends in Ecology & Evolution 22:601−10

doi: 10.1016/j.tree.2007.06.013
[19]

Webster NB, Van Dooren TJM, Schilthuizen M. 2012. Phylogenetic reconstruction and shell evolution of the Diplommatinidae (Gastropoda: Caenogastropoda). Molecular Phylogenetics and Evolution 63(3):625−38

doi: 10.1016/j.ympev.2012.02.004
[20]

Cunha AF, Genzano GN, Marques AC. 2015. Reassessment of morphological diagnostic characters and species boundaries requires taxonomical changes for the genus Orthopyxis L. Agassiz, 1862 (campanulariidae, hydrozoa) and some related campanulariids. PLoS One 10:e0117553

doi: 10.1371/journal.pone.0117553
[21]

Hey J, Fitch WM, Ayala FJ. 2005. Systematics and the origin of species: An introduction. Proceedings of the National Academy of Sciences of the United States of America 102:6515−19

doi: 10.1073/pnas.0501939102
[22]

Jeewon R, Hyde KD. 2016. Establishing species boundaries and new taxa among fungi: recommendations to resolve taxonomic ambiguities. Mycosphere 7:1669−77

doi: 10.5943/mycosphere/7/11/4
[23]

Yang ZL. 2020. Trends in fungal systematics: more and more taxa. Mycosystema 39:1611−16

doi: 10.13346/j.mycosystema.200225
[24]

Hyde KD, Noorabadi MT, Thiyagaraja V, He MQ, Johnston PR, et al. 2024. The 2024 Outline of Fungi and fungus-like taxa. Mycosphere 15:5146−6239

doi: 10.5943/mycosphere/15/1/25
[25]

Wang K, Kirk PM, Yao YJ. 2020. Development trends in taxonomy, with a special reference to fungi. Journal of Systematics and Evolution 58:406−12

doi: 10.1111/jse.12538
[26]

Maharachchikumbura SSN, Chen Y, Ariyawansa HA, Hyde KD, Haelewaters D, et al. 2021. Integrative approaches for species delimitation in Ascomycota. Fungal Diversity 109(1):155−79

doi: 10.1007/s13225-021-00486-6
[27]

Zhao RL, He MQ, Liu JK. 2021. Using divergence time as an additional criterion in fungal systematics. Mycosystema 40:834−43

doi: 10.13346/j.mycosystema.210054
[28]

Zhou LW, May TW. 2023. Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era. Mycology 14:52−59

doi: 10.1080/21501203.2022.2103194
[29]

Wu HX. 2022. Taxonomic Studies on the Fungi of the Microthyriaceae (in Chinese). Yunnan: Yunnan Science and Technology Press. 180 pp

[30]

Morlon H, Robin S, Hartig F. 2022. Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues. Trends in Ecology & Evolution 37:497−506

doi: 10.1016/j.tree.2022.02.004
[31]

Johnston PR, Quijada L, Smith CA, Baral HO, Hosoya T, et al. 2019. A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus 10:1

doi: 10.1186/s43008-019-0002-x
[32]

Ji X, Zhou JL, Song CG, Xu TM, Wu DM, et al. 2022. Taxonomy, phylogeny and divergence times of Polyporus (Basidiomycota) and related genera. Mycosphere 13:1−52

doi: 10.5943/mycosphere/13/1/1
[33]

Sun YF, Xing JH, He XL, Wu DM, Song CG, et al. 2022. Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections. Studies in Mycology 101:287−415

doi: 10.3114/sim.2022.101.05
[34]

Liu S, Sun YF, Ji X, Song CG, Xu TM, et al. 2023. Molecular phylogeny and taxonomy of the remarkable genus Leptoporus (Polyporales, Basidiomycota) with description of a new species from Southwest China. Frontiers in Cellular and Infection Microbiology 12:1116035

doi: 10.3389/fcimb.2022.1116035
[35]

Vandamme AM. 2003. Basic concepts of molecular evolution. In The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. eds. Lemey P, Salemi M, Vandamme AM. UK: Cambridge University Press. pp. 3–30 doi: 10.1017/CBO9780511819049.003

[36]

Godini R, Fallahi H. 2019. A brief overview of the concepts, methods and computational tools used in phylogenetic tree construction and gene prediction. Meta Gene 21:100586

doi: 10.1016/j.mgene.2019.100586
[37]

Huang Y. 2012. Molecular Phylogenetics (in Chinese). Beijing: Science Press. 533 pp

[38]

Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, et al. 2016. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution 94:447−62

doi: 10.1016/j.ympev.2015.10.027
[39]

Pagel M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877−84

doi: 10.1038/44766
[40]

Huelsenbeck JP, Bollback JP. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology 50:351−66

doi: 10.1080/106351501300317978
[41]

Koch NM, Garwood RJ, Parry LA. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings Biological Sciences 288(1950):20210044

doi: 10.1098/rspb.2021.0044
[42]

Roure B, Baurain D, Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Molecular Biology and Evolution 30:197−214

doi: 10.1093/molbev/mss208
[43]

Ryan MJ, Rand AS. 1995. Female responses to ancestral advertisement calls in túngara frogs. Science 269:390−92

doi: 10.1126/science.269.5222.390
[44]

Brusatte SL, Sakamoto M, Montanari S, Harcourt Smith WEH. 2012. The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics. Journal of Evolutionary Biology 25:365−77

doi: 10.1111/j.1420-9101.2011.02427.x
[45]

Simões TR, Caldwell MW, Tałanda M, Bernardi M, Palci A, et al. 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557:706−9

doi: 10.1038/s41586-018-0093-3
[46]

Koh O. 2020. The evolutionary origin of developmental enhancers in vertebrates: Insights from non-model species. Development, Growth & Differentiation 62:326−33

doi: 10.1111/dgd.12662
[47]

Upham NS, Esselstyn JA, Jetz W. 2019. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biology 17(12):e3000494

doi: 10.1371/journal.pbio.3000494
[48]

Schönenberger J, Anderberg AA, Sytsma KJ. 2005. Molecular phylogenetics and patterns of floral evolution in the Ericales. International Journal of Plant Sciences 166:265−88

doi: 10.1086/427198
[49]

Sauquet H, von Balthazar M, Magallón S, Doyle JA, Endress PK, et al. 2017. The ancestral flower of angiosperms and its early diversification. Nature Communications 8:16047

doi: 10.1038/ncomms16047
[50]

Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, et al. 2018. The interrelationships of land plants and the nature of the ancestral embryophyte. Current Biology 28:733−45

doi: 10.1016/j.cub.2018.01.063
[51]

Edwards EJ, Smith SA. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. Proceedings of the National Academy of Sciences of the United States of America 107:2532−37

doi: 10.1073/pnas.0909672107
[52]

Lu LM, Mao LF, Yang T, Ye JF, Liu B, et al. 2018. Evolutionary history of the angiosperm flora of China. Nature 554:234−38

doi: 10.1038/nature25485
[53]

Smith SA, Brown JW. 2018. Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany 105:302−14

doi: 10.1002/ajb2.1019
[54]

Li JC, Wu HX, Li Y, Li XH, Song JY, et al. 2022. Taxonomy, phylogenetic and ancestral area reconstruction in Phyllachora, with four novel species from Northwestern China. Journal of Fungi 8:520

doi: 10.3390/jof8050520
[55]

Rathnayaka AR, Thilini Chethana KW, Phillips AJL, Liu JK, Samarakoon MC, et al. 2023. Re-evaluating Botryosphaeriales: ancestral state reconstructions of selected characters and evolution of nutritional modes. Journal of Fungi 9:184

doi: 10.3390/jof9020184
[56]

Bateson W, Mendel G. 2009. Mendel's Principles of Heredity. UK: Cambridge University Press. 212 pp doi: 10.1017/CBO9780511694462

[57]

Fisher RA. 1919. XV.—The correlation between relatives on the supposition of Mendelian inheritance. Transactions of the Royal Society of Edinburgh 52(2):399−433

doi: 10.1017/S0080456800012163
[58]

Alexopoulos CJ, Mims CW, Blackwell MM. 1996. Introductory Mycology, 4th edition. Wiley Press. 880 pp https://zlib.pub/book/introductory-mycology-3af45coss4bg

[59]

Cseh P, Merényi Z, Bóna L, Varga T, Bóka K, et al. 2024. Taxonomic characterisation of the Regianum clade (genus Tuber) and the trait evolution of spore size among true truffles. Mycological Progress 23:11

doi: 10.1007/s11557-024-01949-1
[60]

Park Y, Metzger BPH, Thornton JW. 2022. Epistatic drift causes gradual decay of predictability in protein evolution. Science 376:823−30

doi: 10.1126/science.abn6895
[61]

Gould SJ, Eldredge N. 1972. Punctuated equilibria: an alternative to phyletic gradualism. In Models in Paleobiology. ed. Schopf TJM. San Francisco: Freeman, Cooper & Company. pp. 82–115 https://www.researchgate.net/publication/221958736_Punctuated_Equilibria_An_Alternative_to_Phyletic_Gradualism

[62]

Stanley SM. 1975. A theory of evolution above the species level. Proceedings of the National Academy of Sciences of the United States of America 72(2):646−50

doi: 10.1073/pnas.72.2.646
[63]

Kumar S. 2005. Molecular clocks: four decades of evolution. Nature Reviews Genetics 6:654−62

doi: 10.1038/nrg1659
[64]

Margoliash E. 1963. Primary structure and evolution of cytochrome C. Proceedings of the National Academy of Sciences of the United States of America 50(4):672−79

doi: 10.1073/pnas.50.4.672
[65]

Grantham T. 2004. The role of fossils in phylogeny reconstruction: why is it so difficult to integrate paleobiological and neontological evolutionary biology? Biology and Philosophy 19:687−720

doi: 10.1007/s10539-005-0370-z
[66]

Felsenstein J. 1985. Phylogenies and the comparative method. The American Naturalist 125:1−15

doi: 10.1086/284325
[67]

Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 20:406−16

doi: 10.1093/sysbio/20.4.406
[68]

Swofford DL, Maddison WP. 1987. Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences 87:199−229

doi: 10.1016/0025-5564(87)90074-5
[69]

Collins TM, Wimberger PH, Naylor GJP. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology 43:482−96

doi: 10.1093/sysbio/43.4.482
[70]

Schluter D, Price T, Mooers AØ, Ludwig D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51(6):1699−711

doi: 10.2307/2410994
[71]

Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754−55

doi: 10.1093/bioinformatics/17.8.754
[72]

Yang Z, Rannala B. 2012. Molecular phylogenetics: principles and practice. Nature Reviews Genetics 13:303−14

doi: 10.1038/nrg3186
[73]

Cunningham CW. 1999. Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses. Systematic Biology 48:665−74

doi: 10.1080/106351599260238
[74]

Omland KE. 1999. The assumptions and challenges of ancestral state reconstructions. Systematic Biology 48:604−11

doi: 10.1080/106351599260175
[75]

Mooers AØ, Schluter D. 1999. Reconstructing ancestor states with maximum likelihood: support for one- and two-rate models. Systematic Biology 48:623−33

doi: 10.1080/106351599260193
[76]

Lewis PO. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913−25

doi: 10.1080/106351501753462876
[77]

Hibbett DS. 2004. Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood: a comparison of binary and multistate approaches. Systematic Biology 53:889−903

doi: 10.1080/10635150490522610
[78]

Schultz TE, Churchill GA. 1999. The role of subjectivity in reconstructing ancestral character states: a Bayesian approach to unknown rates, states and transformation asymmetries. Systematic Biology 48:651−64

doi: 10.1080/106351599260229
[79]

Pagel M, Meade A, Barker D. 2004. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology 53:673−84

doi: 10.1080/10635150490522232
[80]

Ronquist F. 2004. Bayesian inference of character evolution. Trends in Ecology & Evolution 19:475−81

doi: 10.1016/j.tree.2004.07.002
[81]

Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and bayesian approaches over likelihood ratio tests. Systematic Biology 53:793−808

doi: 10.1080/10635150490522304
[82]

Pagel M, Lutzoni F. 2002. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. In Biological Evolution and Statistical Physics. Lecture Notes in Physics, eds. Lässig M, Valleriani A, Vol 585. Berlin, Heidelberg: Springer. pp. 148−61 doi: 10.1007/3-540-45692-9_8

[83]

Pagel M, Meade A. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. The American Naturalist 167:808−25

doi: 10.1086/503444
[84]

Ekman S, Andersen HL, Wedin M. 2008. The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota). Systematic Biology 57:141−56

doi: 10.1080/10635150801910451
[85]

Yu Y, Blair C, He X. 2020. RASP 4: ancestral state reconstruction tool for multiple genes and characters. Molecular Biology and Evolution 37:604−06

doi: 10.1093/molbev/msz257
[86]

Revell LJ. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3(2):217−23

doi: 10.1111/j.2041-210X.2011.00169.x
[87]

Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, et al. 2021. Phylogenetic reassessment, taxonomy, and biogeography of Codinaea and similar fungi. Journal of Fungi 7(12):1097

doi: 10.3390/jof7121097
[88]

Lücking R, Papong K, Thammathaworn A, Boonpragob K. 2008. Historical biogeography and phenotype-phylogeny of Chroodiscus (lichenized Ascomycota: Ostropales: Graphidaceae). Journal of Biogeography 35(12):2311−27

doi: 10.1111/j.1365-2699.2008.01972.x
[89]

Spribille T, Resl P, Stanton DE, Tagirdzhanova G. 2022. Evolutionary biology of lichen symbioses. New Phytologist 234:1566−82

doi: 10.1111/nph.18048
[90]

Floudas D, Binder M, Riley R, Barry K, Blanchette RA, et al. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336:1715−19

doi: 10.1126/science.1221748
[91]

Hibbett DS. 2001. Shiitake mushrooms and molecular clocks: historical biogeography of Lentinula. Journal of Biogeography 28:231−41

doi: 10.1046/j.1365-2699.2001.00528.x
[92]

Wang XW, Jiang JH, Liu SL, Gafforov Y, Zhou LW. 2022. Species diversification of the coniferous pathogenic fungal genus Coniferiporia (Hymenochaetales, Basidiomycota) in association with its biogeography and host plants. Phytopathology 112:404−13

doi: 10.1094/PHYTO-05-21-0181-R
[93]

Aime MC, McTaggart AR, Mondo SJ, Duplessis S. 2017. Phylogenetics and phylogenomics of rust fungi. Advances in Genetics 100:267−307

doi: 10.1016/bs.adgen.2017.09.011
[94]

Kijpornyongpan T, Mondo SJ, Barry K, Sandor L, Lee J, et al. 2018. Broad genomic sampling reveals a smut pathogenic ancestry of the fungal clade Ustilaginomycotina. Molecular Biology and Evolution 35(8):1840−54

doi: 10.1093/molbev/msy072
[95]

Gadd GM. 2006. Fungi in Biogeochemical Cycles. UK: Cambridge University Press. 469 pp doi: 10.1017/CBO9780511550522

[96]

Hawksworth DL, Lücking R. 2017. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiology Spectrum 5(4):10.1128/microbiolspec.funk-0052-2016

doi: 10.1128/microbiolspec.FUNK-0052-2016
[97]

Gargas A, DePriest PT, Grube M, Tehler A. 1995. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268(5216):1492−95

doi: 10.1126/science.7770775
[98]

Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, et al. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484(7393):186−94

doi: 10.1038/nature10947
[99]

Yang Z, Rannala B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution 23(1):212−26

doi: 10.1093/molbev/msj024
[100]

Berbee ML, Taylor JW. 2010. Dating the molecular clock in fungi—how close are we? Fungal Biology Reviews 24(1):1−16

doi: 10.1016/j.fbr.2010.03.001