The importance of fossils in phylogeny reconstruction

A.O. Averianov

Proceedings of the Zoological Institute RAS, 2013, 317(Supplement 2):

Full text  

Abstract

The number of extant species of organisms is approximately 0.5–1% from the total number of species ever lived, which can be estimated as 0.9–1.6 billions. From this number of extant species, only 10% or less is known to the scientists. Thus, a sample of only 0.1% from the total number of species is available for the molecular systematics. This is not enough for an adequate phylogeny of the organic world on the species level based on molecular data. The method of ghost lineages allows quantitative estimation of the fit of the phylogenetic hypotheses to the fossil record. This method is a robust instrument for the testing of the phylogenetic hypothesis. A close coincidence of different measures of ghost lineages for a large number of recent phylogenetic analyses advocates for the adequacy of the fossil record for the understanding of the phylogeny of organic world. Inclusion of fossils into the phylogenetic analysis may dramatically change the topology of the final cladogram, because fossils may bear significant information on the lost evolutionary history. The paleontological data is the only way for calibrating of the molecular clocks. Two thirds of history of life on the Earth is already in the past. Thus, the understanding of the phylogeny of the organic world is not possible without the paleontological data.

Key words

molecular systematics, paleontology, phylogenetic analysis, phylogeny

Published September 16, 2013

References

Angielczyk K.D. and Fox D.L. 2006. Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record. Paleobiology, 32: 147–165. https://doi.org/10.1666/05016.1

Archibald J.D. and Deutschman D.H. 2001. Quantitative analysis of the timing of the origin and diversification of extant placental orders. Journal of Mammalian Evolution, 8: 107–124. https://doi.org/10.1023/A:1011317930838

Benton M.J. and Donoghue P.C.J. 2007. Paleontological evidence to date the tree of life. Molecular Biology and Evolution, 24: 889–891. https://doi.org/10.1093/molbev/msm017

Benton M.J., Wills M.A. and Hitchin R. 2000. Quality of the fossil record through time. Nature, 403: 534–537. https://doi.org/10.1038/35000558

Bourlat S.J., Juliusdottir T., Lowe C.J., Freeman R., Aronowicz J., Kirschner M., Lander E.S., Thorndyke M., Nakano H., Kohn A., Heyland A., Moroz L.L., Copley R.R. and Telford M.J. 2006. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature, 444: 85–88. https://doi.org/10.1038/nature05241

Bryant H.N. 1995. The threefold parallelism of Agassiz and Haeckel, and polarity determination in phylogenetic systematics. Biology and Philosophy, 10: 197–217. https://doi.org/10.1007/BF00852245

Cavin L. and Forey P.L. 2007. Using ghost lineages to identify diversification events in the fossil record. Biology Letters, 3: 201–204. https://doi.org/10.1098/rsbl.2006.0602

Cobbett A., Wilkinson M. and Wills M.A. 2007. Fossils impact as hard as living taxa in parsimony analyses of morphology. Systematic Biology, 56: 753–766. https://doi.org/10.1080/10635150701627296

Conway Morris S. and Collins D.H. 1996. Middle Cambrian ctenophores from the Stephen Formation, British Columbia, Canada. Philosophical Transactions of the Royal Society of London, Series B, 351: 279–308. https://doi.org/10.1098/rstb.1996.0024

Donoghue M.J., Doyle J.A., Gauthier J.A., Kluge A.G. and Rowe T.B. 1989. The importance of fossils in phylogeny reconstruction. Annual Review of Ecology and Systematics, 20: 431–460. https://doi.org/10.1146/annurev.es.20.110189.002243

Douzery E.J.P., Snell E.A., Bapteste E., Delsuc F. and Philippe H. 2004. The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proceedings of the National Academy of Sciences, 101: 15386–15391. https://doi.org/10.1073/pnas.0403984101

Funch P. and Kristensen R.M. 1995. Cycliophora is a new phylum with affinities to Entoprocta and Ectoprocta. Nature, 378: 711–714. https://doi.org/10.1038/378711a0

Gauthier J.A., Kluge A.G. and Rowe T.B. 1988. Amniote phylogeny and the importance of fossils. Cladistics, 4: 105–209. https://doi.org/10.1111/j.1096-0031.1988.tb00514.x

Glansdorff N., Xu Y. and Labedan B. 2008. The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biology Direct, 3: 29. https://doi.org/10.1186/1745-6150-3-29

Heard S.B. and Mooers A.O. 2000. Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proceedings of the Royal Society B: Biological Sciences, 267: 613–620. https://doi.org/10.1098/rspb.2000.1046

Hossfeld U. and Lennart O. 2003. The road from Haeckel: the Jena tradition in evolutionary morphology and the origins of “Evo-Devo”. Biology and Philosophy, 18: 285–307. https://doi.org/10.1023/A:1023988119440

Kidwell S. and Sepkoski J.J., Jr. 1999. The nature of the fossil record. Paleontological Society Special Publication, 9: 61–76. https://doi.org/10.1017/S2475262200014015

Lelièvre H., Bagils R.Z. and Rouget I. 2008. Temporal information, fossil record and phylogeny. Comptes Rendus Palevol, 7: 27–36. https://doi.org/10.1016/j.crpv.2007.12.007

Lepage T., Bryant D., Philippe H. and Lartillot N. 2007. A general comparison of relaxed molecular clock models. Molecular Biology and Evolution, 24: 2669–2680. https://doi.org/10.1093/molbev/msm193

Luo Z.-X. 2007. Transformation and diversification in early mammal evolution. Nature, 450: 1011–1019. https://doi.org/10.1038/nature06277

Lyson T.R., Bever G.S., Bhullar B.-A.S., Joyce W.G. and Gauthier J.A. 2010. Transitional fossils and the origin of turtles. Biology Letters, 6: 830–833. https://doi.org/10.1098/rsbl.2010.0371

Markov A.V. and Korotayev A.V. 2007. Phanerozoic marine biodiversity follows a hyperbolic trend. Palaeoworld, 16: 311–318. https://doi.org/10.1016/j.palwor.2007.01.002

McGowan A.J. and Smith A.B. 2008. Are global Phanerozoic marine diversity curves truly global? A study of the relationship between regional rock records and global Phanerozoic marine diversity. Paleobiology, 34: 80–103. https://doi.org/10.1666/07019.1

Mora C., Tittensor D.P., Adl S., Simpson A.G.B. and Worm B. 2011. How many species are there on Earth and in the Ocean? PLoS Biol, 9: e1001127. https://doi.org/10.1371/journal.pbio.1001127

Nee S. and May R.M. 1997. Extinction and the loss of evolutionary history. Science, 278: 692–694. https://doi.org/10.1126/science.278.5338.692

Peters S.E. and Foote M. 2001. Biodiversity in the Phanerozoic: a reinterpretation. Paleobiology, 27: 583–601. https://doi.org/10.1666/0094-8373(2001)027<0583:BITPAR>2.0.CO;2

Pol D., Norell M.A. and Siddall M.E. 2004. Measures of stratigraphic fit to phylogeny and their sensitivity to tree size, tree shape, and scale. Cladistics, 20: 64–75. https://doi.org/10.1111/j.1096-0031.2003.00002.x

Raup D.M. 1972. Taxonomic diversity during the Phanerozoic. Science, 177: 1065–1071. https://doi.org/10.1126/science.177.4054.1065

Raup D.M. and Stanley S.M. 1971. Principles of Paleontology. San Francisco, Reading, W.H. Freeman and Co. X+388 p.

Smith A.B. 2007. Marine diversity through the Phanerozoic: problems and prospects. Journal of the Geological Society, 164: 731–745. https://doi.org/10.1144/0016/76492006-184

Springer M.S., Burk-Herrick A., Meredith R., Eizirik E., Teeling E.C., O’Brien S.J. and Murphy W.J. 2007. The adequacy of morphology for reconstructing the early history of placental mammals. Systematic Biology, 56: 673–684. https://doi.org/10.1080/10635150701491149

Stanley G.D. and Stürmer W. 1983. The first fossil ctenophore from the Lower Devonian of West Germany. Nature, 303: 518–520. https://doi.org/10.1038/303518a0

Stanley G.D. and Stürmer W. 1987. A new fossil ctenophore discovered by X-rays. Nature, 328: 61–63. https://doi.org/10.1038/328061a0

Theobald D.L. 2010. A formal test of the theory of universal common ancestry. Nature, 465: 219–222. https://doi.org/10.1038/nature09014

Wall P.D., Ivany L.C. and Wilkinson B.H. 2009. Revisiting Raup: exploring the influence of outcrop area on diversity in light of modern sample-standardization techniques. Paleobiology, 35: 146–167. https://doi.org/10.1666/07069.1

Weishampel D.B. 1996. Fossils, phylogeny, and discovery: a cladistic study of the history of tree topologies and ghost lineage durations. Journal of Vertebrate Paleontology, 16: 191–197. https://doi.org/10.1080/02724634.1996.10011307

Wiens J.J. 2003a. Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem? Journal of Vertebrate Paleontology, 23: 297–310. https://doi.org/10.1671/0272-4634(2003)023[0297:ITICAP]2.0.CO;2

Wiens J.J. 2003b. Missing data, incomplete taxa, and phylogenetic accuracy. Systematic Biology, 52: 528–538. https://doi.org/10.1080/10635150390218330

Wiens J.J. and Morrill M.C. 2011. Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Systematic Biology, 60: 719–731. https://doi.org/10.1093/sysbio/syr025

Wilson M.V.H. 1992. Importance for phylogeny of single and multiple stem-group fossil species with examples from freshwater fishes. Systematic Biology, 41: 462–470. https://doi.org/10.1093/sysbio/41.4.462

 

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