A genome evolution-based framework for measures of originality for clades

Journal of Theoretical Biology

Volumn 276, Issue 1, 2011, Pages 99-105

  Huang, Jianxiong ^a,b   Mi, Xiangcheng ^a   Ma, Keping ^a  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Character distribution; Conservation priority; Genome evolution; Originality; Phylogenetics

Indexed keywords

CARNIVORE; CLADISTICS; CONSERVATION GENETICS; EVOLUTION; EXTINCTION; GENOME; PHYLOGENY; WILDLIFE MANAGEMENT;

ARTICLE; BIOLOGICAL TRAIT; CARNIVORA; CLADISTICS; CONCEPTUAL FRAMEWORK; GENE DELETION; GENE INSERTION; GENE MUTATION; GENETIC LINE; GENOME ANALYSIS; GENOME SIZE; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROCESS MODEL; SPECIES CONSERVATION; SPECIES EXTINCTION; SPECIES IDENTIFICATION; SPECIES RARITY; TARGET ORGANISM;

ANIMALS; EVOLUTION, MOLECULAR; GENOME; MODELS, BIOLOGICAL; PHYLOGENY; SPECIES SPECIFICITY;

CARNIVORA;

EID: 79951788550     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.01.037     Document Type: Article

References (41)

1. Altschul S.F., Lipman D.J. Equal animals. Nature 1990, 348:493-494.
2. Bennett P.M., Owens I.P.F Variation in extinction risk among birds: chance or evolutionary predisposition?. Proc. R. Soc. Lond. B-Biol. Sci. 1997, 264:401-408.
3. Bininda-Emonds O.R.P., Gittleman J.L., Purvis A. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 1999, 74:143-175.
4. Barker G.M. Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biol. J. Linn. Soc. 2002, 76:165-194.
5. Cleveland W.S. The Elements of Graphing Data 1994, AT & T Bell Laboratories, Murray Hill, NJ.
6. Crozier R.H. Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annu. Rev. Ecol. Syst. 1997, 28:243-268.
7. Crozier R.H. Genetic diversity and the agony of choice. Biol. Conserv. 1992, 61:11-15.
8. Chessel D., Dufour A.B., Thioulouse J. The ade4 package-I-one-table methods. R News 2004, 4:5-10.
9. Drake J.W. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 1991, 88:7160-7164.
10. Diniz J.A.F., Torres N.M. Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evol. Ecol. 2002, 16:351-367.
11. Faith D.P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 1992, 61:1-10.
12. Faith D.P., Walker P.A. Environmental diversity: on the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas. Biodiversity Conserv. 1996, 5:399-415.
13. Faith D.P. From species to supertrees: popperian corroboration and some current controversies in systematics. Aust. Syst. Bot. 2004, 17:1-16.
14. Humphries C.J., Williams P.H., Vanewright R.I. Measuring biodiversity value for conservation. Annu. Rev. Ecol. Syst. 1995, 26:93-111.
15. Heard S.B., Mooers A.O. Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proc. R. Soc. Lond. B-Biol. Sci. 2000, 267:613-620.
16. Isaac N.J.B., Turvey S.T., Collen B., Waterman C., Baillie J.E.M. Mammals on the EDGE: conservation priorities based on threat and phylogeny. Plos One 2007, 2:e296.
17. IUCN, 2006. IUCN Red List of Threatened Species. 〈〉. http://www.iucnredlist.org.
18. Johnson C.N., Delean S., Balmford A. Phylogeny and the selectivity of extinction in Australian marsupials. Anim. Conserv. 2002, 5:135-142.
19. Johnson W.E., Eizirik E., Pecon-Slattery J., Murphy W.J., Antunes A., Teeling E., O′Brien S.J. The late Miocene radiation of modern Felidae: a genetic assessment. Science 2006, 311:73-77.
20. Kazazian H.H. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
21. Krajewski C. Phylogenetic measures of biodiversity: a comparison and critique. Biol. Conserv. 1994, 69:33-39.
22. Lynch M., Conery J.S. The origins of genome complexity. Science 2003, 302:1401-1404.
23. Long M., Betran E., Thornton K., Wang W. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 2003, 4:865-875.
24. May R.M. Taxonomy as destiny. Nature 1990, 347:129-130.
25. Mooers A.O., Goring S.J., Turvey S., Kuhn T. Holocene extinctions and the loss of feature diversity. Holocene Extinctions 2009, 263-277. Oxford University Press, Oxford, UK. S.T. Turvey (Ed.).
26. Magnuson-Ford K., Ingram T., Redding D.W., Mooers A.O. Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing. Biol. Conserv. 2009, 142:1787-1796.
27. Nixon K.C., Wheeler Q.D. Measures of phylogenetic diversity. Extinction and Phylogeny 1992, 216-234. Columbia University Press, New York. M.J. Novacek, Q.D. Wheeler (Eds.).
28. Oliver M.J., Petrov D., Ackerly D., Falkowski P., Schofield O.M. The mode and tempo of genome size evolution in eukaryotes. Genome Res. 2007, 17:594-601.
29. Pavoine S., Ollier S., Dufour A.B. Is the originality of a species measurable?. Ecol. Lett. 2005, 8:579-586.
30. Petrov D.A. Mutational equilibrium model of genome size evolution. Theor. Popul. Biol. 2002, 61:531-544.
31. Purvis A., Hector A. Getting the measure of biodiversity. Nature 2000, 405:212-219.
32. R Development Core Team R: a Language and Environment for Statistical Computing 2009, R Foundation for Statistical Computing, Vienna, Austria.
33. Redding D.W., Mooers A.O. Incorporating evolutionary measures into conservation prioritization. Conserv. Biol. 2006, 20:1670-1678.
34. Russell G.J., Brooks T.M., McKinney M.M., Anderson C.G. Present and future taxonomic selectivity in bird and mammal extinctions. Conserv. Biol. 1998, 12:1365-1376.
35. Redding D.W., Hartmann K., Mirnoto A., Bokal D., Devos M., Mooers A.O. Evolutionarily distinctive species often capture more phylogenetic diversity than expected. J. Theor. Biol. 2008, 251:606-615.
36. Ricotta C. A parametric diversity measure combining the relative abundances and taxonomic distinctiveness of species. Divers. Distrib. 2004, 10:143-146.
37. Ricklefs R.E. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 2007, 22:601-610.
38. Steel M., Mimoto A., Mooers A.O. Hedging our bets: the expected contribution of species to future phylogenetic diversity. Evol. Bioinform. 2007, 3:237-244.
39. Vane-Wright R.I., Humphries C.J., Williams P.H. What to protect? Systematics and the agony of choice. Biol. Conserv. 1991, 55:235-254.
40. Vamosi J.C., Wilson J.R.U. Nonrandom extinction leads to elevated loss of angiosperm evolutionary history. Ecol. Lett. 2008, 11:1047-1053.
41. Zhu Y.X., Dai J.B., Fuerst P.G., Voytas D.F. Controlling integration specificity of a yeast retrotransposon. Proc. Natl. Acad. Sci. USA 2003, 100:5891-5895.