Volume 44 Issue 6
Nov.  2023
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Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zoological Research, 2023, 44(6): 1064-1079. doi: 10.24272/j.issn.2095-8137.2023.189
Citation: Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zoological Research, 2023, 44(6): 1064-1079. doi: 10.24272/j.issn.2095-8137.2023.189

Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials

doi: 10.24272/j.issn.2095-8137.2023.189
The field-collected Taphozous melanopogon, Aselliscus stoliczkanus, Chaerephon plicatus, and Hipposideros larvatus samples used in this study are not from endangered species and are not included in the “List of Protected Animals in China”. No specific permissions were required for sampling activities.
The generated sequences were submitted to GenBank (accession numbers OR503106–OR504069). Custom Perl scripts and alignments are available at Dryad (DOI: 10.5061/dryad.crjdfn36w).
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
X.M.Z. conceived and supervised the project. J.D., Z.H.L., L.W., X.X.Z., Z.Z., Y.Y., M.L. P.C.W., X.W., and M.L. performed data curation. G.M.L., Q.P., P.F.Z., W.Q.L., C.Y.H., and Y.C.D. conducted hypothesis testing, phylogenetic analyses, and divergence time estimation. G.M.L. and X.M.Z. wrote the manuscript with input from all authors. All authors read and approved the final version of the manuscript.
Funds:  This work was supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China (2021YFC2301300), National Natural Science Foundation of China (82050002, 32070528, 32100335, 32000287), and Beijing Natural Sciences Foundation for Distinguished Young Scholars (JQ19022)
More Information
  • Corresponding author: E-mail: zhouxuming@ioz.ac.cn
  • Received Date: 2023-09-04
  • Accepted Date: 2023-10-23
  • Published Online: 2023-10-25
  • Publish Date: 2023-11-18
  • The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.
  • The field-collected Taphozous melanopogon, Aselliscus stoliczkanus, Chaerephon plicatus, and Hipposideros larvatus samples used in this study are not from endangered species and are not included in the “List of Protected Animals in China”. No specific permissions were required for sampling activities.
    The generated sequences were submitted to GenBank (accession numbers OR503106–OR504069). Custom Perl scripts and alignments are available at Dryad (DOI: 10.5061/dryad.crjdfn36w).
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    X.M.Z. conceived and supervised the project. J.D., Z.H.L., L.W., X.X.Z., Z.Z., Y.Y., M.L. P.C.W., X.W., and M.L. performed data curation. G.M.L., Q.P., P.F.Z., W.Q.L., C.Y.H., and Y.C.D. conducted hypothesis testing, phylogenetic analyses, and divergence time estimation. G.M.L. and X.M.Z. wrote the manuscript with input from all authors. All authors read and approved the final version of the manuscript.
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  • [1]
    Álvarez-Carretero S, Tamuri AU, Battini M, et al. 2022. A species-level timeline of mammal evolution integrating phylogenomic data. Nature, 602(7896): 263−267. doi: 10.1038/s41586-021-04341-1
    [2]
    Archer M, Beck R, Gott M, et al. 2011. Australia's first fossil marsupial mole (Notoryctemorphia) resolves controversies about their evolution and palaeoenvironmental origins. Proceedings of the Royal Society B:Biological Sciences, 278(1711): 1498−1506. doi: 10.1098/rspb.2010.1943
    [3]
    Archibald JD, Deutschman DH. 2001. Quantitative analysis of the timing of the origin and diversification of extant placental orders. Journal of Mammalian Evolution, 8(2): 107−124. doi: 10.1023/A:1011317930838
    [4]
    Arnason U, Gullberg A, Janke A, et al. 2007. Mitogenomic analyses of caniform relationships. Molecular Phylogenetics and Evolution, 45(3): 863−874. doi: 10.1016/j.ympev.2007.06.019
    [5]
    Beck RMD. 2008. A dated phylogeny of marsupials using a molecular supermatrix and multiple fossil constraints. Journal of Mammalogy, 89(1): 175−189. doi: 10.1644/06-MAMM-A-437.1
    [6]
    Beck RMD, Travouillon KJ, Aplin KP, et al. 2014. The osteology and systematics of the enigmatic australian oligo-miocene metatherian Yalkaparidon (Yalkaparidontidae; Yalkaparidontia;? Australidelphia; Marsupialia). Journal of Mammalian Evolution, 21(2): 127−172. doi: 10.1007/s10914-013-9236-3
    [7]
    Betancur-R R, Li CH, Munroe TA, et al. 2013. Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Systematic Biology, 62(5): 763−785. doi: 10.1093/sysbio/syt039
    [8]
    Bininda-Emonds ORP, Cardillo M, Jones KE, et al. 2007. The delayed rise of present-day mammals. Nature, 446(7135): 507−512. doi: 10.1038/nature05634
    [9]
    Blanga-Kanfi S, Miranda H, Penn O, et al. 2009. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evolutionary Biology, 9(1): 71. doi: 10.1186/1471-2148-9-71
    [10]
    Brace S, Thomas JA, Dalén L, et al. 2016. Evolutionary history of the Nesophontidae, the last unplaced recent mammal family. Molecular Biology and Evolution, 33(12): 3095−3103. doi: 10.1093/molbev/msw186
    [11]
    Chen MY, Liang D, Zhang P. 2017. Phylogenomic resolution of the phylogeny of Laurasiatherian mammals: exploring phylogenetic signals within coding and noncoding sequences. Genome Biology and Evolution, 9(8): 1998−2012. doi: 10.1093/gbe/evx147
    [12]
    Chen Z, Xu SX, Zhou KY, et al. 2011. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences. BMC Evolutionary Biology, 11(1): 314. doi: 10.1186/1471-2148-11-314
    [13]
    Churakov G, Sadasivuni MK, Rosenbloom KR, et al. 2010. Rodent evolution: back to the root. Molecular Biology and Evolution, 27(6): 1315−1326. doi: 10.1093/molbev/msq019
    [14]
    Collins TM, Fedrigo O, Naylor GJ. 2005. Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Systematic Biology, 54(3): 493−500. doi: 10.1080/10635150590947339
    [15]
    Delsuc F, Ranwez V. 2020. Accurate alignment of (meta)barcoding data sets using MACSE. In: Scornavacca C, Delsuc F, Galtier N. Phylogenetics in the Genomic Era. No Commercial Publisher, 2.3: 1–2.3: 31.
    [16]
    Di Franco A, Poujol R, Baurain D, et al. 2019. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evolutionary Biology, 19(1): 21. doi: 10.1186/s12862-019-1350-2
    [17]
    Dilcher D. 2000. Toward a new synthesis: major evolutionary trends in the angiosperm fossil record. Proceedings of the National Academy of Sciences of the United States of America, 97(13): 7030−7036.
    [18]
    Doronina L, Churakov G, Kuritzin A, et al. 2017a. Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Research, 27(6): 997−1003. doi: 10.1101/gr.210948.116
    [19]
    Doronina L, Churakov G, Shi JJ, et al. 2015. Exploring massive incomplete lineage sorting in arctoids (Laurasiatheria, Carnivora). Molecular Biology and Evolution, 32(12): 3194−3204.
    [20]
    Doronina L, Feigin CY, Schmitz J. 2022. Reunion of Australasian possums by shared SINE insertions. Systematic Biology, 71(5): 1045−1053. doi: 10.1093/sysbio/syac025
    [21]
    Doronina L, Matzke A, Churakov G, et al. 2017b. The beaver’s phylogenetic lineage illuminated by retroposon reads. Scientific Reports, 7(1): 43562. doi: 10.1038/srep43562
    [22]
    dos Reis M, Donoghue PCJ, Yang ZH. 2014. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biology Letters, 10(1): 20131003. doi: 10.1098/rsbl.2013.1003
    [23]
    dos Reis M, Donoghue PCJ, Yang ZH. 2016. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics, 17(2): 71−80. doi: 10.1038/nrg.2015.8
    [24]
    dos Reis M, Inoue J, Hasegawa M, et al. 2012. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society B: Biological Sciences, 279(1742): 3491−3500. doi: 10.1098/rspb.2012.0683
    [25]
    dos Reis M, Thawornwattana Y, Angelis K, et al. 2015. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Current Biology, 25(22): 2939−2950. doi: 10.1016/j.cub.2015.09.066
    [26]
    dos Reis MD, Gunnell GF, Barba-Montoya J, et al. 2018. Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case. Systematic Biology, 67(4): 594−615. doi: 10.1093/sysbio/syy001
    [27]
    Duchêne DA, Bragg JG, Duchêne S, et al. 2018. Analysis of phylogenomic tree space resolves relationships among marsupial families. Systematic Biology, 67(3): 400−412. doi: 10.1093/sysbio/syx076
    [28]
    Duff A, Lawson A. 2004. Mammals of the World. A Checklist. London: A and C Black.
    [29]
    Edwards SV. 2009. Is a new and general theory of molecular systematics emerging?. Evolution, 63(1): 1−19. doi: 10.1111/j.1558-5646.2008.00549.x
    [30]
    Emerling CA, Huynh HT, Nguyen MA, et al. 2015. Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution. Proceedings of the Royal Society B:Biological Sciences, 282(1819): 20151817. doi: 10.1098/rspb.2015.1817
    [31]
    Esselstyn JA, Oliveros CH, Swanson MT, et al. 2017. Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements. Genome Biology and Evolution, 9(9): 2308−2321. doi: 10.1093/gbe/evx168
    [32]
    Etienne RS, Pigot AL, Phillimore AB. 2016. How reliably can we infer diversity-dependent diversification from phylogenies?. Methods in Ecology and Evolution, 7(9): 1092−1099. doi: 10.1111/2041-210X.12565
    [33]
    Feijoo M, Parada A. 2017. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage. Molecular Phylogenetics and Evolution, 113: 76−83. doi: 10.1016/j.ympev.2017.05.004
    [34]
    Foley NM, Mason VC, Harris AJ, et al. 2023. A genomic timescale for placental mammal evolution. Science, 380(6643): eabl8189. doi: 10.1126/science.abl8189
    [35]
    Foley NM, Springer MS, Teeling EC. 2016. Mammal madness: is the mammal tree of life not yet resolved?. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1699): 20150140. doi: 10.1098/rstb.2015.0140
    [36]
    Gatesy J, Meredith RW, Janecka JE, et al. 2017. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia. Cladistics, 33(3): 295−332. doi: 10.1111/cla.12170
    [37]
    Gatesy J, Springer MS. 2017. Phylogenomic red flags: homology errors and zombie lineages in the evolutionary diversification of placental mammals. Proceedings of the National Academy of Sciences of the United States of America, 114(45): E9431−E9432.
    [38]
    Grossnickle DM, Newham E. 2016. Therian mammals experience an ecomorphological radiation during the Late Cretaceous and selective extinction at the K-Pg boundary. Proceedings of the Royal Society B:Biological Sciences, 283(1832): 20160256. doi: 10.1098/rspb.2016.0256
    [39]
    Gu ZG, Eils R, Schlesner M. 2016. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18): 2847−2849. doi: 10.1093/bioinformatics/btw313
    [40]
    Guo YT, Zhang J, Xu DM, et al. 2021. Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae. Zoological Research, 42(5): 671−674. doi: 10.24272/j.issn.2095-8137.2021.240
    [41]
    He K, Chen X, Chen P, et al. 2018. A new genus of Asiatic short-tailed shrew (Soricidae, Eulipotyphla) based on molecular and morphological comparisons. Zoological Research, 39(5): 321−334. doi: 10.24272/j.issn.2095-8137.2018.058
    [42]
    Höhna S, Landis MJ, Heath TA, et al. 2016. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Systematic Biology, 65(4): 726−736. doi: 10.1093/sysbio/syw021
    [43]
    Hu JY, Zhang YP, Yu L. 2012. Summary of Laurasiatheria (Mammalia) phylogeny. Zoological Research, 33(E5-6): 65−74.
    [44]
    Huerta-Cepas J, Serra F, Bork P. 2016. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Molecular Biology and Evolution, 33(6): 1635−1638. doi: 10.1093/molbev/msw046
    [45]
    International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature, 409(6822): 860−921. doi: 10.1038/35057062
    [46]
    Ivanova NV, Clare EL, Borisenko AV. 2012. DNA barcoding in mammals. In: Kress WJ, Erickson DL. DNA Barcodes. Totowa: Humana Press, 153–182.
    [47]
    Jebb D, Huang ZX, Pippel M, et al. 2020. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583(7817): 578−584. doi: 10.1038/s41586-020-2486-3
    [48]
    Katoh K, Misawa K, Kuma KI, et al. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14): 3059−3066. doi: 10.1093/nar/gkf436
    [49]
    Kay RF, Macfadden BJ, Madden RH, et al. 1998. Revised age of the Salla beds, Bolivia, and its bearing on the age of the Deseadan South American Land Mammal “Age”. Journal of Vertebrate Paleontology, 18(1): 189−199. doi: 10.1080/02724634.1998.10011043
    [50]
    Kozlov AM, Darriba D, Flouri T, et al. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21): 4453−4455. doi: 10.1093/bioinformatics/btz305
    [51]
    Lambert O, Martínez-Cáceres M, Bianucci G, et al. 2017. Earliest mysticete from the Late Eocene of Peru sheds new light on the origin of baleen whales. Current Biology, 27(10): 1535−1541.e2. doi: 10.1016/j.cub.2017.04.026
    [52]
    Lanfear R, Frandsen PB, Wright AM, et al. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34(3): 772−773.
    [53]
    Lavergne A, Douzery E, Stichler T, et al. 1996. Interordinal mammalian relationships: evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences. Molecular Phylogenetics and Evolution, 6(2): 245−258. doi: 10.1006/mpev.1996.0074
    [54]
    Lee MSY, Hugall AF. 2003. Partitioned likelihood support and the evaluation of data set conflict. Systematic Biology, 52(1): 15−22. doi: 10.1080/10635150390132650
    [55]
    Lin JN, Chen GF, Gu L, et al. 2014. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate. Molecular Phylogenetics and Evolution, 71: 193−200. doi: 10.1016/j.ympev.2013.12.001
    [56]
    Liu L, Zhang J, Rheindt FE, et al. 2017. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proceedings of the National Academy of Sciences of the United States of America, 114(35): E7282−E7290.
    [57]
    Lv X, Hu JY, Hu YW, et al. 2021. Diverse phylogenomic datasets uncover a concordant scenario of Laurasiatherian interordinal relationships. Molecular Phylogenetics and Evolution, 157: 107065. doi: 10.1016/j.ympev.2020.107065
    [58]
    Magallón S, Gómez-Acevedo S, Sánchez-Reyes L, et al. 2015. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytologist, 207(2): 437−453. doi: 10.1111/nph.13264
    [59]
    Maliet O, Hartig F, Morlon H. 2019. A model with many small shifts for estimating species-specific diversification rates. Nature Ecology & Evolution, 3(7): 1086−1092.
    [60]
    May-Collado LJ, Kilpatrick CW, Agnarsson I. 2015. Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria). PeerJ, 3: e805. doi: 10.7717/peerj.805
    [61]
    McCormack JE, Faircloth BC, Crawford NG, et al. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Research, 22(4): 746−754. doi: 10.1101/gr.125864.111
    [62]
    McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, et al. 2020. Phylogenomic resolution of the cetacean tree of life using target sequence capture. Systematic Biology, 69(3): 479−501. doi: 10.1093/sysbio/syz068
    [63]
    Meredith RW, Janečka JE, Gatesy J, et al. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science, 334(6055): 521−524. doi: 10.1126/science.1211028
    [64]
    Meredith RW, Westerman M, Springer MS. 2009. A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes. Molecular Phylogenetics and Evolution, 51(3): 554−571. doi: 10.1016/j.ympev.2009.02.009
    [65]
    Meyer CP. 2003. Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biological Journal of the Linnean Society, 79(3): 401−459. doi: 10.1046/j.1095-8312.2003.00197.x
    [66]
    Minh BQ, Schmidt HA, Chernomor O, et al. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37(5): 1530−1534. doi: 10.1093/molbev/msaa015
    [67]
    Missoup AD, Yemchui GD, Denys C, et al. 2018. Molecular phylogenetic analyses indicate paraphyly of the genus Hybomys (Rodentia: Muridae): taxonomic implications. Journal of Zoological Systematics and Evolutionary Research, 56(3): 444−452. doi: 10.1111/jzs.12213
    [68]
    Mitchell KJ, Pratt RC, Watson LN, et al. 2014. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31(9): 2322−2330. doi: 10.1093/molbev/msu176
    [69]
    Montgelard C, Forty E, Arnal V, et al. 2008. Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments. BMC Evolutionary Biology, 8(1): 321. doi: 10.1186/1471-2148-8-321
    [70]
    Morlon H, Lewitus E, Condamine FL, et al. 2016. RPANDA: an R package for macroevolutionary analyses on phylogenetic trees. Methods in Ecology and Evolution, 7(5): 589−597. doi: 10.1111/2041-210X.12526
    [71]
    Murata Y, Nikaido M, Sasaki T, et al. 2003. Afrotherian phylogeny as inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution, 28(2): 253−260. doi: 10.1016/S1055-7903(03)00035-6
    [72]
    Murphy WJ, Foley NM, Bredemeyer KR, et al. 2021. Phylogenomics and the genetic architecture of the placental mammal Radiation. Annual Review of Animal Biosciences, 9: 29−53. doi: 10.1146/annurev-animal-061220-023149
    [73]
    Nabholz B, Künstner A, Wang R, et al. 2011. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Molecular Biology and Evolution, 28(8): 2197−2210. doi: 10.1093/molbev/msr047
    [74]
    Narita Y, Oda SI, Takenaka O, et al. 2001. Phylogenetic position of Eulipotyphla inferred from the cDNA sequences of pepsinogens A and C. Molecular Phylogenetics and Evolution, 21(1): 32−42. doi: 10.1006/mpev.2001.0996
    [75]
    Nishihara H, Satta Y, Nikaido M, et al. 2005. A retroposon analysis of Afrotherian phylogeny. Molecular Biology and Evolution, 22(9): 1823−1833. doi: 10.1093/molbev/msi179
    [76]
    Phillips MJ. 2016. Geomolecular dating and the origin of placental mammals. Systematic Biology, 65(3): 546−557. doi: 10.1093/sysbio/syv115
    [77]
    Phillips MJ, Pratt RC. 2008. Family-level relationships among the Australasian marsupial “herbivores” (Diprotodontia: Koala, wombats, kangaroos and possums). Molecular Phylogenetics and Evolution, 46(2): 594−605. doi: 10.1016/j.ympev.2007.09.008
    [78]
    Politis DN, Romano JP. 1994. The stationary bootstrap. Journal of the American Statistical Association, 89(428): 1303−1313. doi: 10.1080/01621459.1994.10476870
    [79]
    Puttick MN, Thomas GH. 2015. Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria. Proceedings of the Royal Society B: Biological Sciences, 282(1821): 20152023. doi: 10.1098/rspb.2015.2023
    [80]
    Puttick MN, Thomas GH, Benton MJ. 2016. Dating placentalia: morphological clocks fail to close the molecular fossil gap. Evolution, 70(4): 873−886. doi: 10.1111/evo.12907
    [81]
    Rabosky DL. 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution, 60(6): 1152−1164.
    [82]
    Rabosky DL, Grundler M, Anderson C, et al. 2014. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods in Ecology and Evolution, 5(7): 701−707. doi: 10.1111/2041-210X.12199
    [83]
    Ranwez V, Douzery EJP, Cambon C, et al. 2018. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Molecular Biology and Evolution, 35(10): 2582−2584. doi: 10.1093/molbev/msy159
    [84]
    Rodríguez-Ezpeleta N, Brinkmann H, Roure B, et al. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Systematic Biology, 56(3): 389−399. doi: 10.1080/10635150701397643
    [85]
    Romiguier J, Ranwez V, Delsuc F, et al. 2013a. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Molecular Biology and Evolution, 30(9): 2134−2144. doi: 10.1093/molbev/mst116
    [86]
    Romiguier J, Ranwez V, Douzery EJP, et al. 2013b. Genomic evidence for large, long-lived ancestors to placental mammals. Molecular Biology and Evolution, 30(1): 5−13. doi: 10.1093/molbev/mss211
    [87]
    Ronquist F, Teslenko M, van der Mark P, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3): 539−542. doi: 10.1093/sysbio/sys029
    [88]
    Sato JJ, Bradford TM, Armstrong KN, et al. 2019. Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements. Molecular Phylogenetics and Evolution, 141: 106605. doi: 10.1016/j.ympev.2019.106605
    [89]
    Sayyari E, Whitfield JB, Mirarab S. 2018. DiscoVista: interpretable visualizations of gene tree discordance. Molecular Phylogenetics and Evolution, 122: 110−115. doi: 10.1016/j.ympev.2018.01.019
    [90]
    Scornavacca C, Belkhir K, Lopez J, et al. 2019. OrthoMaM v10: scaling-up orthologous coding sequence and exon alignments with more than one hundred mammalian genomes. Molecular Biology and Evolution, 36(4): 861−862. doi: 10.1093/molbev/msz015
    [91]
    Scornavacca C, Galtier N. 2017. Incomplete lineage sorting in mammalian phylogenomics. Systematic Biology, 66(1): 112−120.
    [92]
    Shen XX, Hittinger CT, Rokas A. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution, 1(5): 0126.
    [93]
    Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16(8): 1114. doi: 10.1093/oxfordjournals.molbev.a026201
    [94]
    Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 17(12): 1246−1247. doi: 10.1093/bioinformatics/17.12.1246
    [95]
    Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51(3): 492−508. doi: 10.1080/10635150290069913
    [96]
    Song S, Liu L, Edwards SV, et al. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proceedings of the National Academy of Sciences of the United States of America, 109(37): 14942−14947.
    [97]
    Springer MS, Emerling CA, Meredith RW, et al. 2017. Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Molecular Phylogenetics and Evolution, 106: 86−102. doi: 10.1016/j.ympev.2016.09.017
    [98]
    Springer MS, Foley NM, Brady PL, et al. 2019. Evolutionary models for the diversification of placental mammals across the KPg boundary. Frontiers in Genetics, 10: 1241. doi: 10.3389/fgene.2019.01241
    [99]
    Springer MS, Murphy WJ, Eizirik E, et al. 2003. Placental mammal diversification and the Cretaceous–Tertiary boundary. Proceedings of the National Academy of Sciences of the United States of America, 100(3): 1056−1061.
    [100]
    Springer MS, Woodburne MO. 1989. The distribution of some basicranial characters within the Marsupialia and a phylogeny of the Phalangeriformes. Journal of Vertebrate Paleontology, 9(2): 210−221. doi: 10.1080/02724634.1989.10011755
    [101]
    Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9): 1312−1313. doi: 10.1093/bioinformatics/btu033
    [102]
    Steenwyk JL, Buida III TJ, Labella AL, et al. 2021. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics, 37(16): 2325−2331. doi: 10.1093/bioinformatics/btab096
    [103]
    Steppan SJ, Adkins RM, Anderson J. 2004. Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Systematic Biology, 53(4): 533−553. doi: 10.1080/10635150490468701
    [104]
    Steppan SJ, Schenk JJ. 2017. Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates. PLoS One, 12(8): e0183070. doi: 10.1371/journal.pone.0183070
    [105]
    Swanson MT, Oliveros CH, Esselstyn JA. 2019. A phylogenomic rodent tree reveals the repeated evolution of masseter architectures. Proceedings of the Royal Society B: Biological Sciences, 286(1902): 20190672. doi: 10.1098/rspb.2019.0672
    [106]
    Tarver JE, dos Reis M, Mirarab S, et al. 2016. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, 8(2): 330−344. doi: 10.1093/gbe/evv261
    [107]
    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
    [108]
    Wible JR, Rougier GW, Novacek MJ, et al. 2007. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary. Nature, 447(7147): 1003−1006. doi: 10.1038/nature05854
    [109]
    Wickham H, Chang W, Wickham MH. 2016. Package ‘ggplot2’. Create Elegant Data Visualisations Using the Grammar of Graphics. Version, 2(1): 1−189.
    [110]
    Wildman DE, Jameson NM, Opazo JC, et al. 2009. A fully resolved genus level phylogeny of neotropical primates (Platyrrhini). Molecular Phylogenetics and Evolution, 53(3): 694−702. doi: 10.1016/j.ympev.2009.07.019
    [111]
    Yang ZH. 1994. Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution, 39(1): 105−111.
    [112]
    Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586−1591. doi: 10.1093/molbev/msm088
    [113]
    Yu L, Luan PT, Jin W, et al. 2011. Phylogenetic utility of nuclear introns in interfamilial relationships of Caniformia (order Carnivora). Systematic Biology, 60(2): 175−187. doi: 10.1093/sysbio/syq090
    [114]
    Zhang C, Sayyari E, Mirarab S. 2017. ASTRAL-III: increased scalability and impacts of contracting low support branches. In: Proceedings of the 15th International Workshop on RECOMB International Workshop on Comparative Genomics. Barcelona, Spain: Springer, 53–75.
    [115]
    Zhou XM, Xu SX, Xu JX, et al. 2012. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. Systematic Biology, 61(1): 150. doi: 10.1093/sysbio/syr089
    [116]
    Zhou XM, Xu SX, Yang YX, et al. 2011. Phylogenomic analyses and improved resolution of Cetartiodactyla. Molecular Phylogenetics and Evolution, 61(2): 255−264. doi: 10.1016/j.ympev.2011.02.009
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