Deep-time phylogenetic clustering of extinctions in an evolutionarily dynamic clade (early jurassic ammonites)

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Hardy, Clotilde ^a   Fara, Emmanuel ^a   Laffont, Rémi ^a   Dommergues, Jean Louis ^a   Meister, Christian ^b   Neige, Pascal ^a  

^a UNIVERSITÉ DE BOURGOGNE   (France)

^b MUSÉUM D HISTOIRE NATURELLE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONITE; CEPHALOPOD; CLADISTICS; CLUSTER ANALYSIS; CONSERVATION BIOLOGY; EVOLUTION; GEOLOGICAL TIME; LOWER JURASSIC; NONHUMAN; PHYLOGENY; PLIENSBACHIAN; REVIEW; SPECIES EXTINCTION; SURVIVAL;

ANIMALS; BIOLOGICAL EVOLUTION; CEPHALOPODA; CLUSTER ANALYSIS; EXTINCTION, BIOLOGICAL; FOSSILS; MODELS, STATISTICAL; PHYLOGENY;

AMMONOIDEA; CEPHALOPODA;

EID: 84861475304     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037977     Document Type: Review

References (58)

1. Escarguel G, Fara E, Brayard A, Legendre S, (2011) Biodiversity is not (and never has been) a bed of roses! C R Biol 334: 351-359 (DOI 10.1016/j.crvi.2011.02.006).
2. Purvis A, (2008) Phylogenetic approaches to the study of extinction. Annu Rev Ecol Syst 39 301-319. (DOI 10.1146/annurev-ecolsys-063008-102010).
3. Roy K, Hunt G, Jablonski D, (2009) Phylogenetic conservatism of extinctions in marine bivalves. Science 325 733-737. (DOI 10.1126/science.1173073).
4. Raup DM, (1991) Extinction: bad genes or bad luck? New York W. W. Norton.
5. McKinney ML, (1997) Extinction vulnerability and selectivity: Combining ecological and paleontological views. Annu Rev Ecol Syst 28 495-516. (DOI 10.1146/annurev.ecolsys.28.1.495).
6. Bennett PM, Owens IPF, (1997) Variation in extinction risk among birds: Chance or evolutionary predisposition? Proc R Soc B 264 401-408. (DOI 10.1098/rspb.1997.0057).
7. Russell GJ, Brooks TM, McKinney MM, Anderson CG, (1998) Present and future taxonomic selectivity in bird and mammal extinctions. Conserv Biol 12 1365-1376. (DOI 10.1111/j.1523-1739.1998.96332.x).
8. Purvis A, Cardillo M, Grenyer R, Collen B, (2005) Correlates of extinction risk: phylogeny, biology, threat and scale. In: Purvis A, Gittleman JL, Brooks T, editors. Phylogeny and conservation Cambridge Cambridge University Press pp. 295-316.
9. Bielby J, Cunningham AA, Purvis A, (2006) Taxonomic selectivity in amphibians: ignorance, geography or biology? Anim Conserv 9 135-143. (DOI 10.1111/j.1469-1795.2005.00013.x).
10. Davies TJ, Fritz SA, Grenyer R, Orme CDL, Bielby J, et al. (2008) Phylogenetic trees and the future of mammalian biodiversity. Proc Natl Acad Sci USA 105 11556-11563. (DOI 10.1073/pnas.0801917105).
11. Green WA, Hunt G, Wing SL, DiMichele WA, (2011) Does extinction wield an axe or pruning shears? How interactions between phylogeny and ecology affect patterns of extinction. Paleobiology 37 72-91. (DOI 10.1666/09078.1).
12. Purvis A, Agapow PM, Gittleman JL, Mace GM, (2000) Nonrandom extinction and the loss of evolutionary history. Science 288 328-330. (DOI 10.1126/science.288.5464.328).
13. Cardillo M, Mace GM, Jones KE, Bielby J, Bininda-Emonds ORP, et al. (2005) Multiple causes of high extinction risk in large mammal species. Science 309 1239-1241. (DOI 10.1126/science.1116030).
14. Harnik PG, (2011) Direct and indirect effects of biological factors on extinction risk in fossil bivalves. PNAS 108 13594-13599. (DOI 10.1073/pnas.1100572108).
15. Heard SB, Mooers AO, (2000) Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proc R Soc B 267 613-620. (DOI 10.1098/rspb.2000.1046).
16. Diniz-Filho JAF, (2004) Phylogenetic autocorrelation analysis of extinction risks and the loss of evolutionary history in Felidae (Carnivora: Mammalia). Evol Ecol 18 273-282. (DOI 10.1023/BEVEC.0000035072.54176.5a).
17. Erwin DH, (2008) Extinction as the loss of evolutionary history. Proc Natl Acad Sci USA 105 11520-11527. (DOI 10.1073/pnas.0801913105).
18. Parhar RK, Mooers AØ, (2011) Phylogenetically clustered extinction risks do not substantially prune the tree of life. PLoS ONE 6 e23528. (DOI 10.1371/journal.pone.0023528).
19. Gittleman JL, Kot M, (1990) Adaptation: statistics and a null model for estimating phylogenetic effects. Syst Zool 39: 227-241.
20. Lockwood JL, Russell GJ, Gittleman JL, Daehler CC, McKinney ML, et al. (2002) A metric for analyzing taxonomic patterns of extinction risk. Conserv Biol 16 1137-1142. (DOI 10.1046/j.1523-1739.2002.01152.x).
21. Corey SJ, Waite TA, (2008) Phylogenetic autocorrelation of extinction threat in globally imperilled amphibians. Diversity Distrib 14 614-629. (DOI 10.1111/j.1472-4642.2007.00448.x).
22. Sjöström A, Gross CL, (2006) Life-history characters and phylogeny are correlated with extinction risk in the Australian angiosperms. J Biogeogr 33 271-290. (DOI 10.1111/j.1365-2699.2005.01393.x).
23. Fritz SA, Purvis A, (2010) Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conserv Biol 24 1042-1051. (DOI 10.1111/j.1523-1739.2010.01455.x).
24. Gradstein FM, Ogg JG, Smith AG, (2004) A geologic time scale 2004, Cambridge: Cambridge University Press.
25. Ogg JG, Ogg G, Gradstein FM, (2008) The concise Geologic Time scale. Cambridge Cambridge University Press.
26. Rosales I, Quesada S Robles S, (2004) Paleotemperature variations of Early Jurassic seawater recorded in geochemical trends of belemnites from the Basque-Cantabrian basin, northern Spain. Palaeogeog Palaeoclim Palaeoecol 203 253-275. (DOI 10.1016/S0031-0182(03)00686-2).
27. Dera G, Pucéat E, Pellenard P, Neige P, Delsate D, et al. (2009) Water mass exchange and variations in seawater temperature in the NW Tethys during the Early Jurassic: Evidence from neodymium and oxygen isotopes of fish teeth and belemnites. Earth Planet Sci Lett 286 198-207. (DOI 10.1016/j.epsl.2009.06.027).
28. Doyle P, (1994) Aspects of the distribution of Lower Jurassic belemnites. Palaeopelagos 1: 109-121.
29. Dommergues J-L, (1997) Le Jurassique inférieur. Cariou E, Hantzpergue P editors Biostratigraphie du Jurassique ouest-européen et méditerranéen: zonations parallèles et distribution des invertébrés et microfossiles Bulletin du Centre Recherche, Elf Exploration et Production, Pau, Mémoire no. 17 pp. 347-353.
30. Meister C, Stampfli G, (2000) Les ammonites du Lias moyen (Pliensbachien) de la Néotéthys et de ses confins; compositions fauniques, affinités paléogéographiques et biodiversité. Rev Paléobiol 19: 227-292.
31. Dommergues J-L, Laurin B, Meister C, (2001) The recovery and radiation of Early Jurassic ammonoids: morphologic versus palaeobiogeographical patterns. Palaeogeog Palaeoclim Palaeoecol 165 195-213. (DOI 10.1016/S0031-0182(00)00160-7).
32. Dommergues J-L, Fara E, Meister C, (2009) Ammonite diversity and its palaeobiogeographical structure during the early Pliensbachian (Jurassic) in the western Tethys and adjacent areas. Palaeogeog Palaeoclim Palaeoecol 280 64-77. (DOI 10.1016/j.palaeo.2009.06.005).
33. Dera G, Neige P, Dommergues J-L, Fara E, Laffont R, et al. (2010) High-resolution dynamics of Early Jurassic marine extinctions: the case of Pliensbachian-Toarcian ammonites (Cephalopoda). J Geol Soc Lond 167 21-33. (DOI 10.1144/0016-76492009-068).
34. Davis RA, Landman NH, Dommergues JL, Marchand D, Bucher H, (1996) Mature modifications and dimorphism in ammonoid cephalopods. In: Landman NH, Tanabe K, Davis RA, editors. Ammonoid Paleobiology Topics in Geobiology 13. New York Plenum Press pp. 463-539.
35. Dommergues J-L, Meister C, (1999) Cladistic formalisation of relationships within a superfamily of Lower Jurassic Ammonitina: Eoderocerataceae SPATH, 1929. Rev Paléobiol 18: 273-286.
36. Venturi F, Bilotta M, (2008) New data and hypotheses on early Jurassic ammonite phylogeny. Rev Paléobiol 27 (2): 859-901.
37. Venturi F, Rea G, Silvestrini G, Bilotta M, (2010) Ammoniti: un viaggio geologico nelle montagne appenniniche.
38. Hoffmann R, (2010) New insights on the phylogeny of the Lytoceratoidea (Ammonitina) from the septal lobe and its functional interpretation. Rev Paléobiol 29: 1-156.
39. Bilotta M, (2010) Aequiloboidea: A new Early Jurassic ammonite superfamily of the Mediterranean Tethys. Geobios 43: 581-604.
40. Dommergues J-L, Guiffray A, Dumont Th, Chevalier F, (2011) La lumachelle à Cardinia (Bivalves) et Alsatites (Ammonites) du «Revers de Côte Dure» dans l'Hettangien de la couverture sédimentaire du Massif du Rochail (Oisans, Isère, France). Rev Paléobiol 30: 193-221.
41. Dommergues J-L, Meister C, (2012) Significance of intermediate forms in phyletic reconstruction of ammonites: Early Jurassic Phricodoceras case study. Acta Palaeontol Pol In press. (DOI dx.doi.org/10.4202/ app.2011.0148).
42. Izsák J, Papp L, (1995) Application of the quadratic entropy indices for diversity studies of drosophilid assemblages. Environ Ecol Stat 2 213-224. (DOI 10.1007/BF00456668).
43. Clarke KR, Warwick RM, (1998) A taxonomic distinctness index and its statistical properties. J Appl Ecol 35, 523-531. (DOI 10.1046/j.1365-2664.1998.3540523.x).
44. Ricotta C, (2004) A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species. Diversity Distrib 10 143-146. (DOI 10.1111/j.1366-9516.2004.00069.x).
45. Moran PAP, (1950) Notes on Continuous Stochastic Phenomena. Biometrika 37 17-23. (DOI 10.1093/biomet/37.1-2.17).
46. Gittleman JL, Anderson CG, Gates SE, Luh HK, Smith JD, (1998) Detecting Ecological Pattem in Phylogenies. In: McKinney ML, Drake JA, editors. Biodiversity Dynamics: Turnover of Populations, Taxa, and Communities New York Columbia University Press pp. 51-69.
47. Diniz-Filho JAF, (2001) Phylogenetic autocorrelation under distinct evolutionary processes. Evolution 55 1104-1109. (DOI 10.1111/j.0014-3820.2001.tb00630.x.
48. Upton GJG, Fingleton B, (1985) Spatial data analysis by example. New York Wiley.
49. Pavoine S, Ollier S, Pontier D, Chessel D, (2008) Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theor Popul Biol 73 79-91. (DOI 10.1016/j.tpb.2007.10.001).
50. Legendre P, Legendre L, (1998) Numerical Ecology, 2nd edn. Amsterdam Elsevier Science.
51. Fortin M-J, Dale MRT, (2005) Spatial Analysis: A Guide for Ecologists Cambridge: Cambridge University Press.
52. Guilford J, (1936) Psychometric Methods. New York McGraw-Hill. Book Company.
53. R Development Core Team 2010 R: a language and environment for statistical computing, version 2.12.0 Vienna, Austria: R Foundation for Statistical Computing. See R website. 2 Available: http://www.R-project.org. Accessed 2012 May.
54. Orme D, Freckleton R, Thomas G, Petzoldt T, Fritz S, (2008) CAIC: comparative analyses using independent contrasts. R package version 1.0.4-94.
55. Paradis E, Claude J, Strimmer K, (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20 289-290. (DOI 10.1093/bioinformatics/btg412).
56. Cooper N, Bielby J, Thomas GH, Purvis A, (2007) Macroecology and extinction risk correlates of frogs. Global Ecol Biogeogr 17 211-221. (DOI 10.1111/j.1466-8238.2007.00355.x).
57. Dommergues J-L, El Hariri K, (2002) Endemism as a palaeobiogeographic parameter of basin history illustrated by early- and mid-Liassic peri-Tethyan ammonite faunas. Palaeogeog Palaeoclim Palaeoecol 184 407-418. (DOI 10.1016/S0031-0182(02)00276-6).
58. Jones KE, Purvis A, Gittleman JL, (2003) Biological correlates of extinction risk in bats. Am Nat 161 601-614. (DOI 10.1086/368289).