A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Yedid, Gabriel ^a   Stredwick, Jason ^b   Ofria, Charles A ^c   Agapow, Paul Michael ^d  

^a UNIVERSITY OF OSLO   (Norway)

^b UTest   (United States)

^c Michigan State University   (United States)

^d PUBLIC HEALTH ENGLAND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AGE DISTRIBUTION; ARTICLE; COMMUNITY STRUCTURE; CONTROLLED STUDY; DIGITAL ORGANISM; ENVIRONMENTAL EROSION; HISTORY; MASS EXTINCTION; ORGANISMS; PHYLOGENETIC TREE; POPULATION RECOVERY; RANDOM MASS EXTINCTION; SELECTIVE MASS EXTINCTION; SPECIES DIFFERENTIATION; BIOLOGICAL MODEL; COMPARATIVE STUDY; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; GENETIC SELECTION; MOLECULAR EVOLUTION; PHYLOGENY; SPECIES EXTINCTION; STATISTICS;

ECOLOGICAL AND ENVIRONMENTAL PROCESSES; EVOLUTION, MOLECULAR; EXTINCTION, BIOLOGICAL; MODELS, BIOLOGICAL; PHYLOGENY; SELECTION, GENETIC; STOCHASTIC PROCESSES;

EID: 84861675543     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037233     Document Type: Article

References (56)

1. Heywood VH, eds. (1995) Global Biodiversity and Assessment. New York, New York Cambridge University Press.
2. Pimm SL, Russell GJ, Gittleman JL, Brooks TM, (1995) The future of biodiversity. Science 269: 347-350.
3. Russell GJ, Brooks TM, McKinney ML, Anderson CG, (1998) Present and future taxonomic selectivity in bird and mammal extinctions. Cons Biol 12: 1365-1376.
4. Purvis A, Agapow P-M, Gittleman JL, Mace GM, (2000) Nonrandom extinction and the loss of evolutionary history. Science 288: 328-330.
5. von Euler F, (2001) Selective extinction and rapid loss of evolutionary history in the bird fauna. Proc R Soc Lond B 268: 127-130.
6. Nee S, (2005) Phylogenetic futures after the latest mass extinction. In: Purvis A, Gittleman J, Brooks T (eds.), Phylogeny and Conservation. Cambridge, UK: Cambridge University Press, 387-399.
7. Nee S, May RM, (1997) Extinction and the loss of evolutionary history. Science 278: 692-694.
8. Erwin DH, (2008) Extinction as the loss of evolutionary history. Proc Natl Acad Sci U S A 105 (Suppl. 1): 11520-11527.
9. Harvey PH, May RM, Nee S, (1994) Phylogenies without fossils. Evolution 48: 523-529.
10. Nee S, Holmes EC, May RM, Harvey PH, (1995) Estimating extinction from molecular phylogenies. In: Lawton JH, May RM (eds.), Extinction rates. Oxford, UK: Oxford University Press, 164-182.
11. Goldstein DB, Harvey PH, (1999) Evolutionary inference from genomic data. BioEssays 21: 148-156.
12. Crisp MD, Cook LG, (2009) Explosive radiation or mass extinction? Interpreting signatures in molecular phylogenies. Evolution 63: 2257-2265.
13. Bambach RK, Knoll AH, Wang SC, (2004) Origination, extinction, and mass depletions of marine diversity. Paleobiology 30: 522-542.
14. Bambach RK, (2006) Phanerozoic biodiversity mass extinctions. Ann Rev Earth Plan Sci 34: 127-155.
15. Heard SB, Mooers AØ, (2000) Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proc R Soc Lond B 267: 613-620.
16. Heard SB, Mooers AØ, (2002) Signatures of random and selective mass extinction in phylogenetic tree balance. Syst Biol 51: 889-897.
17. Vamosi JC, Wilson JRU, (2008) Nonrandom extinction leads to elevated loss of angiosperm evolutionary history. Ecol Lett 11: 1047-1053.
18. Fritz SA, Purvis A, (2010) Phylogenetic diversity does not capture body size variation at risk in the world's mammals. Proc R Soc Lond B 277: 2435-2441.
19. Harcourt-Brown KG, (2002) Tree balance, time slices, and evolutionary turnover in Cretaceous planktonic Foraminifera. Syst Biol 51: 908-916.
20. Carlson SJ, (2008) Tree balance, clade size distribution and extinction selectivity in Paleozoic terebratulide brachiopods. Fossils and Strata 54: 167-172.
21. Yedid G, Ofria CA, Lenski RE, (2009) Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms. Am Nat 173: E139-E154.
22. Quental TB, Marshall CR, (2009) Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution 63: 3158-3167.
23. Liow LH, Quental TB, Marshall CR, (2010) When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Syst Biol 59: 646-659.
24. Ofria C, Wilke CO, (2004) Avida: a software platform for research in computational evolutionary biology. Artificial Life 10: 191-229.
25. Lenski RE, Ofria C, Collier TC, Adami C, (1999) Genome complexity, robustness and genetic interactions in digital organisms. Nature 400: 661-664.
26. Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C, (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331-333.
27. Elena SF, Sanjuan R, (2008) The effect of genetic robustness on evolvability in digital organisms. BMC Evo Bio 8: 284.
28. Lenski RE, Ofria, C, Pennock, RT, Adami C, (2003) The evolutionary origin of complex features. Nature 423: 139-144.
29. Yedid G, Ofria CA, Lenski RE, (2008) Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms. J Evol Biol 21: 1335-1357.
30. Cooper TF, Ofria C, (2003) Evolution of stable ecosystems in populations of digital organisms. In: Standish RK, Bedau MA, and Abbass HA, eds. Eighth International Conference on Artificial Life, December 9-13, Sydney, New South Wales. Cambridge, MA: MIT Press, 227-232.
31. Chow S, Wilke CO, Ofria C, Lenski RE, Adami C, (2004) Adaptive radiation from resource competition in digital organisms. Science 305: 84-86.
32. Ostrowski EA, Ofria C, Lenski RE, (2007) Ecological specialization and adaptive decay in digital organisms. Am Nat 169: E1-E20.
33. Misevic D, Ofria C, Lenski RE, (2010) Experiments with digital organisms on the origin and maintenance of sex in changing environments. J Hered 101 (Supp 1): S46-S54.
34. Hang D-H, Torng E, Ofria C, Schmidt TM, (2007) The effect of natural selection on the performance of maximum parsimony. BMC Evo Bio 7: 94.
35. Sole RV, Montoya JM, Erwin DH, (2002) Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics. Phil Trans Roy Soc B 357: 697-707.
36. Roopnarine PD, (2006) Extinction cascades and catastrophes in ancient food webs. Paleobiology 32: 1-19.
37. Roopnarine PD, Angielczyk KD, Wang SC, Hertog R, (2007) Trophic network models explain instability of Early Triassic terrestrial communities. Proc Roy Soc B 274: 2077-2086.
38. Roopnarine PD, (2009) Ecological modeling of paleocommunity food webs. In: Dietl GP, Flessa KW eds. Conservation Paleobiology: Using the Past to Manage For the Future, Paleontological Short Course, Oct. 17, 2009. The Paleontological Society Papers, vol. 15. Boulder, CO: The Paleontological Society, 195-220.
39. Sole RV, Saldaña J, Montoya JM, Erwin DH, (2010) Simple model of recovery after mass extinction. J Theor Bio 267: 193-200.
40. Benton MJ, Twitchett RJ, (2003) How to kill (almost) all life: the end-Permian extinction event. Trends Ecol Evol 18: 358-365.
41. Sahney S, Benton MJ, (2008) Recovery from the most profound mass extinction of all time. Proc Roy Soc B 275: 759-765.
42. Simpson GG, (1951) The species concept. Evolution 5: 285-298.
43. Barraclough TG, Birky CW Jr, Burt A, (2003) Diversification in sexual and asexual organisms. Evolution 57: 2166-2172.
44. McPeek MA, (2008) The ecological dynamics of clade diversification and community assembly. Am Nat 172: E270-E284.
45. Erwin DH, (1998) The end and the beginning: recoveries from mass extinctions. Trends Ecol Evol 13: 344-349.
46. McGowan AJ, (2004) The effect of the Permo-Triassic bottleneck on Triassic ammonoid morphological evolution. Paleobiology 30: 369-395.
47. Pybus OG, Harvey PH, (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc R Soc Lond B 267: 2267-2272.
48. Phillimore AB, Price TD, (2008) Density-dependent cladogenesis in birds. PLoS Biol 6 (3): 483-489.
49. Rohlf FJ, Chang WS, Sokal RR, Kim J, (1990) Accuracy of estimated phylogenies: effects of tree topology and evolutionary model. Evolution 44: 1671-1684.
50. MATLAB R2010b, v7.11. Sunderland, Massachusetts Sinauer Associates.
51. Vamosi JC, Vamosi SM, (2005) Present day risk of extinction may exacerbate the lower species richness of dioecious clades. Div Distrib 11: 25-32.
52. Jablonski D, (2002) Survival without recovery after mass extinctions. Proc Natl Acad Sci U S A 99: 8139-8144.
53. Jablonski D, (2001) Lessons from the past: evolutionary impacts of mass extinctions. Proc Natl Acad Sci U S A 98: 5393-5398.
54. Jablonski D, (2005) Mass extinctions and macroevolution. Paleobiology 31: 192-210.
55. McKinney ML, (1997) Extinction vulnerability and selectivity: combining ecological and paleontological views. Ann Rev Ecol Syst 28: 495-516.
56. McGhee GR Jr, Sheehan PM, Bottjer DJ, Droser ML, (2004) Ecological ranking of Phanerozoic biodiversity crises: ecological and taxonomic severities are decoupled. Palaeogeog Palaeoclim Palaeoecol 211: 289-297.