Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

Abstract

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 63

1. 1.

   Alroy J (2010 ) The shifting balance of diversity among major marine animal groups. Science 321: 1191–1194.

   Not in our library10.1126/science.1189910 (opens in a new tab)

2. 2.

   Sepkoski JJ (1978 ) A kinetic model of Phanerozoic taxonomic diversity I. Analysis of marine orders. Paleobiology 4: 223–251.

   Not in our library

3. 3.

   Mittelbach GG, Schemske DW, Cornell HV, Allen AP, Brown JM, et al (2007 ) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology Letters 10: 315–331.

   Not in our library10.1111/j.1461-0248.2007.01020.x (opens in a new tab)

4. 4.

   Ricklefs RE (1987 ) Community diversity - relative roles of local and regional processes. Science 235: 167–171.

   Not in our library10.1126/science.235.4785.167 (opens in a new tab)

5. 5.

   Glor RE (2010 ) Phylogenetic insights on adaptive radiation. Ann Rev Ecol Evol Syst 41: 251–270.

   Not in our library

6. 6.

   Morlon H, Parsons TL, Plotkin JB (2011 ) Reconciling molecular phylogenies with the fossil record. Proceedings of the National Academy of Sciences of the United States of America 108: 16327–16332.

   Not in our library10.1073/pnas.1102543108 (opens in a new tab)

7. 7.

   Paradis E (2011 ) Time-dependent speciation and extinction from phylogenies: a least squares approach. Evolution 65: 661–672.

   Not in our library10.1111/j.1558-5646.2010.01179.x (opens in a new tab)

8. 8.

   Ricklefs RE (2007 ) Estimating diversification rates from phylogenetic information. Trends in Ecology & Evolution 22: 601–610.

   Not in our library10.1016/j.tree.2007.06.013 (opens in a new tab)

9. 9.

   Wagner CE, Harmon LJ, Seehausen O (2012 ) Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487: 366–369.

   Not in our library10.1038/nature11144 (opens in a new tab)

10. 10.

    Alroy J (2008 ) The dynamics of origination and extinction in the marine fossil record. Proc Nat Acad Sci USA 105: 11536–11542.

    Not in our library10.1073/pnas.0802597105 (opens in a new tab)

11. 11.

    Foote M (2000 ) Origination and extinction components of taxonomic diversity: general problems. Paleobiology 26: 74–102.

    Not in our library

12. 12.

    Nee S, May RM, Harvey PH (1994 ) The reconstructed evolutionary process. Phil Trans R Soc Lond B Biol Sci 344: 305–311.

    Not in our library10.1098/rstb.1994.0068 (opens in a new tab)

13. 13.

    Etienne RS, Haegeman B, Stadler T, Aze T, Pearson PN, et al (2012 ) Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc R Soc Lond B Biol Sci 279: 1300–1309.

    Not in our library10.1098/rspb.2011.1439 (opens in a new tab)

14. 14.

    Rabosky DL, Lovette IJ (2008 ) Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time? Evolution 62: 1866–1875.

    Not in our library10.1111/j.1558-5646.2008.00409.x (opens in a new tab)

15. 15.

    Stadler T (2011 ) Mammalian phylogeny reveals recent diversification rate shifts. Proc Natl Acad Sci USA 108: 6187–6192.

    Not in our library10.1073/pnas.1016876108 (opens in a new tab)

16. 16.

    McPeek MA (2008 ) Ecological dynamics of clade diversification and community assembly. Am Nat 172: E270–E284.

    Not in our library10.1086/593137 (opens in a new tab)

17. 17.
    Inferring the Dynamics of Diversification: A Coalescent Approach · 2010

    No notice
18. 18.
    Density-Dependent Cladogenesis in Birds · 2008

    No notice
19. 19.

    Ruber L, Zardoya R (2005 ) Rapid cladogenesis in marine fishes revisited. Evolution 59: 1119–1127.

    Not in our library

20. 20.

    Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, et al (2009 ) Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Nat Acad Sci USA 106: 13410–13414.

    Not in our library10.1073/pnas.0811087106 (opens in a new tab)

21. 21.

    Slowinski JB, Guyer CG (1989 ) Testing the stochasticity of patterns of organismal diversity: an imporoved null model. American Naturalist 134: 907–921.

    Not in our library

22. 22.

    FitzJohn R (2010 ) Quantitative traits and diversification. Syst Biol 59: 619–633.

    Not in our library10.1093/sysbio/syq053 (opens in a new tab)

23. 23.

    Maddison WP, Midford PE, Otto SP (2007 ) Estimating a binary character’s effect on speciation and extinction. Syst Biol 56: 701–710.

    Not in our library10.1080/10635150701607033 (opens in a new tab)

24. 24.

    Mitter C, Farrell B, Wiegmann B (1988 ) The phylogenetic study of adaptive zones - has phytophagy promoted insect diversification? American Naturalist 132: 107–128.

    Not in our library

25. 25.

    Paradis E (2005 ) Statistical analysis of diversification with species traits. Evolution 59: 1–12.

    Not in our library

26. 26.

    Rabosky DL, Glor RE (2010 ) Equilibrium speciation dynamics in a model adaptive radiation of island lizards. Proc Nat Acad Sci USA 107: 22178–22183.

    Not in our library10.1073/pnas.1007606107 (opens in a new tab)

27. 27.

    Rabosky DL (2010 ) Extinction rates should not be estimated from molecular phylogenies. Evolution 64: 1816–1824.

    Not in our library10.1111/j.1558-5646.2009.00926.x (opens in a new tab)

28. 28.

    Rabosky DL (2012 ) Testing the time-for-speciation effect in the assembly of regional biotas. Methods Ecol Evol 3: 224–233.

    Not in our library

29. 29.

    Jonnson KA, Fabre P–H, Fritz SA, Etienne RS, Ricklefs RE, et al (2012 ) Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas. Proc Natl Acad Sci USA 109: 6620–6625.

    Not in our library10.1073/pnas.1115835109 (opens in a new tab)

30. 30.

    Huelsenbeck JP, Larget B, Swofford D (2000 ) A compound Poisson process for relaxing the molecular clock. Genetics 154: 1879–1892.

    Not in our library10.1093/genetics/154.4.1879 (opens in a new tab)

31. 31.

    Green PJ (1995 ) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711–732.

    Not in our library

32. 32.

    Rabosky DL, Donnellan SC, Talaba AL, Lovette IJ (2007 ) Exceptional among-lineage variation in diversification rates during the radiation of Australia’s most diverse vertebrate clade. Proc R Soc Lond B Biol Sci 274: 2915–2923.

    Not in our library10.1098/rspb.2007.0924 (opens in a new tab)

33. 33.

    Bartolucci F, Scaccia L, Mira A (2006 ) Efficient Bayes factor estimation from the reversible jump output. Biometrika 93: 41–52.

    Not in our library

34. 34.

    Quental TB, Marshall CR (2009 ) Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution 63: 3158–3167.

    Not in our library10.1111/j.1558-5646.2009.00794.x (opens in a new tab)

35. 35.

    Bokma F (2008 ) Detection of “punctuated equilibrium” by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62: 2718–2726.

    Not in our library10.1111/j.1558-5646.2008.00492.x (opens in a new tab)

36. 36.

    Silvestro D, Schnitzler J, Zizka G (2011 ) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evol Biol 11: 311.

    Not in our library10.1186/1471-2148-11-311 (opens in a new tab)

37. 37.

    Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ (2011 ) A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65: 3578–3589.

    Not in our library10.1111/j.1558-5646.2011.01401.x (opens in a new tab)

38. 38.

    Venditti C, Meade A, Pagel M (2011 ) Multiple routes to mammalian diversity. Nature 479: 393–396.

    Not in our library10.1038/nature10516 (opens in a new tab)

39. 39.

    Hastings WK (1970 ) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97–109.

    Not in our library

40. 40.

    Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953 ) Equations of state calculations by fast computing machines. J Chem Phys 21: 1087–1091.

    Not in our library

Cited by papers we hold 15

• Phylogenomics and the rise of the angiosperms · 2024
  No notice
• phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) · 2024
  No notice
• A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins · 2023
  No notice
• Ecological and evolutionary trends of body size in Pristimantis frogs, the world's most diverse vertebrate genus · 2022
  Not checked
• Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation · 2019
  No notice
• Contemporaneous radiations of fungi and plants linked to symbiosis · 2018
  No notice
• Evolutionary history of Coleoptera revealed by extensive sampling of genes and species · 2018
  No notice
• Macroecology and macroevolution of the latitudinal diversity gradient in ants · 2018
  No notice
• Spatio-temporal evolution of Allium L. in the Qinghai–Tibet-Plateau region: Immigration and in situ radiation · 2017
  Not checked
• Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot · 2017
  No notice
• Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates · 2017
  No notice
• Viviparity stimulates diversification in an order of fish · 2016
  Not checked
• The abiotic and biotic drivers of rapid diversification in A ndean bellflowers (Campanulaceae) · 2016
  No notice
• Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating · 2015
  No notice
• Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies · 2015
  No notice

Questions about this paper

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.