Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

Systematic Biology

Volumn 65, Issue 4, 2016, Pages 628-639

  Stadler, Tanja ^a,b   Degnan, James H ^c   Rosenberg, Noah A ^d  

^a ETH ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF NEW MEXICO   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

Birth death process; Genealogy; Multispecies coalescent; Phylogeny

Indexed keywords

BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; PHYLOGENY; PROCEDURES; SPECIES DIFFERENTIATION; TIME;

CLASSIFICATION; COMPUTER SIMULATION; GENETIC SPECIATION; MODELS, BIOLOGICAL; PHYLOGENY; TIME;

EID: 84979233669     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syw019     Document Type: Article

References (55)

1. Agapow P.M., Purvis A. 2002. Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst. Biol. 51:866-872.
2. Aldous D., Pemantle R., editors. 1996. Random discrete structures, vol. 76 of The IMA volumes in mathematics and its applications. Springer, New York; p. 1-18.
3. Aldous D., Popovic L. 2005. A critical branching process model for biodiversity. Adv. Appl. Prob. 37:1094-1115.
4. Aldous D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statist. Sci. 16:23-34.
5. Blum M.G.B., Francois O. 2006. Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance. Syst. Biol. 55:685-691.
6. Bokma F., van den Brink V., Stadler T. 2012. Unexpectedly many extinct hominins. Evolution 66:2969-2974.
7. Bortolussi N., Durand E., Blum M., Francois O. 2006. Aptreeshape: statistical analysis of phylogenetic tree shape. Bioinformatics 22:363-364.
8. Burgess R., Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25:1979-1994.
9. Colless D.H. 1982. Phylogenetics: the theory and practice of phylogenetic systematics. Syst. Zool. 31:100-104.
10. DeGiorgio M., Syring J., Eckert A.J., Liston A., Cronn R., Neale D.B., Rosenberg N.A. 2014. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol. Biol. 14:67.
11. Degnan J.H. 2013. Anomalous unrooted gene trees. Syst. Biol. 62: 574-590.
12. Degnan J.H., Rosenberg N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24:332-340.
13. Degnan J.H., Rosenberg N.A., Stadler T. 2012. The probability distribution of ranked gene trees on a species tree. Math. Biosci. 235:245-255.
14. Degnan J.H., Salter L.A. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37.
15. Drummond A.J., Rambaut A., Shapiro B., Pybus O.G. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22:1185-1192.
16. Ebersberger I., Galgoczy P., Taudien S., Taenzer S., Platzer M., von Haeseler A. 2007. Mapping human genetic ancestry. Mol. Biol. Evol. 24:2266-2277.
17. Edwards S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
18. Etienne R.S., Rosindell J. 2012. Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst. Biol. 61:204-213.
19. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer.
20. Gernhard T. 2008a. The conditioned reconstructed process. J. Theor. Biol. 253:769-778.
21. Gernhard T. 2008b.Newanalytic results for speciation times in neutral models. Bull. Math. Biol. 70:1082-1097.
22. Hagen O., Hartmann K., Steel M., Stadler T. 2015. Age-dependent speciation can explain the shape ofempirical phylogenies. Syst. Biol. 64:432-440.
23. Harvey P.H., May R.M., Nee S. 1994. Phylogenies without fossils. Evolution 48:523-529.
24. Heard S.B. 1996. Patterns in phylogenetic tree balance with variable and evolving speciation rates. Evolution 50:2141-2148.
25. HeardS.B., MooersA.O. 2002. Signatures of randomand selectivemass extinctions in phylogenetic tree balance. Syst. Biol. 51:889-897.
26. HeathT.A., Zwickl D.J.,KimJ., Hillis D.M. 2008.Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57:160-166.
27. Hobolth A., Dutheil J.Y., Hawks J., Schierup M.H., Mailund T. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 21:349-356.
28. Holton T.A., Wilkinson M., Pisani D. 2014. The shape of modern tree reconstruction methods. Syst. Biol. 63:436-441.
29. Hudson R.R. 1990. Gene genealogies and the coalescent process. Oxford Surv. Evol. Biol. 7:1-44.
30. Kendall D.G. 1948. On some modes of population growth leading to R. A. Fisher's logarithmic series distribution. Biometrika 35:6-15.
31. Kendall D.G. 1949. Stochastic processes and population growth. J. Roy. Statist. Soc. Ser. B. 11:230-264.
32. Kingman J.F.C. 1982a. The coalescent. Stoch. Proc. Appl. 13:235-248.
33. Kingman J.F.C. 1982b. On the genealogy of large populations. J. Appl. Prob. 19A:27-43.
34. Liu L., Wu S., Yu L. 2015. Coalescent methods for estimating species trees from phylogenomic data. J. Syst. Evol. 53:380-390.
35. Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
36. McKenzie A., Steel M. 2000. Distributions of cherries for two models of trees. Math. Biosci. 164:81-92.
37. Mooers A., Gascuel O., Stadler T., Li H., Steel M. 2012. Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Syst. Biol. 61:195-203.
38. Mooers A.O., Heard S.B. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54.
39. Nee S., May R.M., Harvey P.H. 1994. The reconstructed evolutionary process. Phil. Trans. R. Soc. Lond. B 344:305-311.
40. Ogilvie H.A., Heled J., Xie D., Drummond A.J. 2016. Computational performance and statistical accuracy of ∗Beast and comparisons with other methods. Syst. Biol. doi: 10.1093/sysbio/syv118.
41. Pybus O.G., Harvey P.H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267:2267-2272.
42. Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes usingDNA sequences from multiple loci. Genetics 164:1645-1656.
43. Sackin M.J. 1972. "Good" and "bad" phenograms. Syst. Zool. 21: 225-226.
44. Sanderson M.J., Donoghue M.J., PielW., Eriksson T. 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am. J. Bot. 81:183.
45. Schrago C.G. 2014. The effective population sizes of the anthropoid ancestors of the human-chimpanzee lineage provide insights on the historical biogeography of the great apes. Mol. Biol. Evol. 31:37-47.
46. Stadler T. 2008. Lineages-through-time plots of neutral models for speciation. Math. Biosci. 216:163-171.
47. Stadler T. 2009. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261:58-66.
48. Stadler T. 2011. Simulating trees with a fixed number of extant species. Syst. Biol. 60:676-684.
49. Stadler T. 2013. Recovering speciation and extinction dynamics based on phylogenies. J. Evol. Biol. 26:1203-1219.
50. Stadler T., Steel M. 2012. Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models. J. Theor. Biol. 297:33-40.
51. Szollosi G.J., Tannier E., Daubin V., Boussau B. 2015. The inference of gene trees with species trees. Syst. Biol. 64:e42-e62.
52. Than C., Nakhleh L. 2009. Species tree inference by minimizing deep coalescences. PLoS Comput. Biol. 5:e1000501.
53. Than C.V., Rosenberg, N.A. 2014. Mean deep coalescence cost under exchangeable probability distributions. Discrete Appl. Math. 174: 11-26.
54. Wu Y. 2012. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66:763-775.
55. Zhu S., Degnan J.H., Goldstien S.J., Eldon B. 2015. Hybridlambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. BMC Bioinform. 16:292.