Measurement of biological information with applications from genes to landscapes

Molecular Ecology

Volumn 15, Issue 10, 2006, Pages 2857-2869

  Sherwin, William B ^a,b   Jabot, Franck ^a,c   Rush, Rebecca ^a   Rossetto, Maurizio ^d  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^c ECOLE POLYTECHNIQUE   (France)

^d ROYAL BOTANIC GARDENS AND DOMAIN TRUST   (Australia)

Author keywords

Biodiversity; Dispersal; Population genetics; Shannon information; Subdivision

Indexed keywords

ALLELE; ANIMAL; ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; GENE; GENETICS; MUTATION; POPULATION DENSITY; SPECIES DIFFERENTIATION;

ALLELES; ANIMALS; BIODIVERSITY; GENES, PLANT; GENETIC SPECIATION; MODELS, GENETIC; MUTATION; POPULATION DENSITY;

EID: 33747039208     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.02992.x     Document Type: Article

References (66)

1. Allen JD (1975) Components of diversity. Oecologia, 18, 359-367.
2. Baker AJ, Moeed A (1987) Rapid genetic differentiation and founder effect in colonizing populations of common mynahs (Acridotheres tristis). Evolution, 41, 525-538.
3. Balloux F (2001) EASYPOP (version 1.7): a computer program for population genetics. Journal of Heredity, 92, 301-302.
4. Beaumont M, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics, 162, 2025.
5. Beerli P, Felsenstein J (1999) Maximum likelihood estimation of migration rates and population numbers of two populations using a coalescent approach. Genetics, 152, 763-773.
6. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA, 98, 4563-4568.
7. Bell D (1968) Information Theory. Pitman, London.
8. Berry O, Tocher MD, Sarre SD (2004) Can assignment tests measure dispersal? Molecular Ecology, 13, 551-561.
9. Brookes MI, Graneau YA, King P et al. (1997) Genetic analysis of founder bottlenecks in the rare British butterfly Plebejus argus. Conservation Biology, 11, 648-661.
10. Buddle CM, Beguin J, Bolduc E et al. (2004) The importance and use of taxon sampling curves for comparative biodiversity research with forest arthropod assemblages. Canadian Entomologist, 137, 120-127.
11. Bussell JD (1999) The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Molecular Ecology, 8, 775-789.
12. Crist TO, Veech JA, Gering JC, Summerville KS (2003) Partitioning species diversity across landscapes and regions: a hierarchical analysis of α, β and γ diversity. American Naturalist, 162, 734-743.
13. England PR, Briscoe DA, Frankham R (1996) Microsatellite polymorphisms in a wild population of Drosophila melanogaster. Genetical Research, 67, 285-290.
14. England PR, Osler GHR, Woodworth LM et al. (2003) Effects of intense versus diffuse population bottlenecks on microsatellite genetic diversity and evolutionary potential. Conservation Genetics, 4, 595-604.
15. Etienne RS, Olff H (2004) A novel genealogical approach to neutral biodiversity theory. Ecology Letters, 7, 170-175.
16. Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87-112.
17. Fisher RA, Corbet AS, Williams CB (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. J. Anim. Ecol., 12, 42-58.
18. Frankham R, Gilligan DM, Morris D, Briscoe DA (2001) Inbreeding and extinction: effects of purging. Conservation Genetics, 2, 279-285.
19. Gilligan DM, Frankham R (2003) Dynamics of genetic adaptation to captivity. Conservation Genetics, 4, 189-197.
20. Goudet J, Raymond M, De Meeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics and Molecular Biology, 144, 1933-1940.
21. Hartl GB, Willing R, Nadlinger K (1994) Allozymes in mammalian population genetics and systematics: indicative function of a marker system reconsidered. In: Molecular Ecology and Evolution: Approaches and Applications (eds Schierwater B, Streit B, Wagner GP, De Salle R) Experientia Supplementum 69, 299-310.
22. He F, Hu XS (2005) Hubbell's fundamental biodiversity parameter and the Simpson diversity index. Ecology Letters, 8, 386-390.
23. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.
24. Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology, 54, 427-432.
25. Hubalek Z (2000) Measures of species diversity in ecology: an evaluation. Folia Zoologica, 49, 241-260.
26. Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, New Jersey.
27. Johnston MS (1988) Founder effects and geographic variation in the land snail Theba pisana. Heredity, 61, 133-142.
28. Keylock CJ (2005) Simpson diversity and the Shannon/Wiener index as special cases of a generalized entropy. Oikos, 109, 203-207.
29. Kimura M, Ohta T (1975) Distribution of allele frequencies in a finite population under stepwise production of neutral alleles. Proceedings of the National Academy of Sciences, USA, 72, 2761-2764.
30. Krebs CJ (1985) Ecology: The Experimental Analysis of Distribution and Abundance. Harper & Row, New York.
31. Lacerda DR, Acedo MDP, Lemos Filho JP, Lovato MB (2001) Genetic diversity and structure of natural populations of Plathymenia reticulata (Mimosoideae), a tropical tree from the Brazilian Cerrado. Molecular Ecology, 10, 1143-1152.
32. Lande R (1996) Statistics and partitioning of species diversity and similarity among multiple communities. Oikos, 76, 5-13.
33. Lande R, DeVries PJ, Walla TR (2000) When species accumulation curves intersect: implications for ranking diversity using small samples. Oikos, 89, 601-605.
34. Lewontin RC (1972) The apportionment of human diversity. Evolutionary Biology, 6, 381-398.
35. Long JC, Naidu JM, Mohrenweiser HW et al. (1986) Genetic charaterisation of Gainj- and Kalam-speaking peoples of Papua New Guinea. American Journal of Physical Anthrolopology, 70, 75-96.
36. MacNally R (1996) Hierarchical partitioning as an interpretative tool in multivariate inference. Australian Journal of Ecology, 21, 224-228.
37. Magurran AE (2004) Measuring Biological Diversity. Blackwell, Oxford.
38. May RM (1981) Patterns in multispecies communities. In: Theoretical Ecology: Principles and Applications (ed. May RM), pp. 142-162. Blackwell, Oxford.
39. Mouillot D, Lepretre A (1999) A comparison of species diversity estimators. Researches in Population Ecology, 41, 203-215.
40. Nei M, Maruyama T, Chakraborty R (1975) Bottleneck effect and genetic-variability in populations. Evolution, 29, 1-10.
41. Ovenden JR, White RWG (1990) Mitochondrial and allozyme genetics of incipient speciation in a landlocked population of Galaxias truttaceus (Pisces: Galaxiidae). Genetics, 124, 701-716.
42. Pavoine S, Dolédec S (2005) The apportionment of quadratic entropy: a useful alternative for partitioning diversity in ecological data. Environmental and Ecological Statistics, 12, 125-138.
43. ST: analysis of population data for conservation. Conservation Genetics, 5, 585-602.
44. Pielou EC (1966) The measurement of diversity in different types of biological collections. Journal of Theoretical Biology, 13, 131-144.
45. Preston FW (1948) The commonness, and rasity, of species. Ecology Letters, 29, 254-283.
46. Rannala B, Hartigan JA (1996) Estimating gene flow in island populations. Genetical Research, 67, 147-115.
47. Raymond M, Rousset F (1995) GENEPOP (version 1.2): a population genetics software for exact test and ecumenism. Journal of Heredity, 86, 248-249.
48. Reyes-Valdes M, Williams CG (2005) An entropy-based measure of founder informativeness. Genetical Research, 85, 81-88.
49. Ricotta C (2003) Additive partition of parametric information and its associated β-diversity measure. Acta Biotheoretica, 51, 91-100.
50. Rogan PK, Schneider TD (1995) Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites. Human Mutation, 6, 74-76.
51. Rossetto M, Jones R, Hunter J (2004) Genetic effects of rainforest fragmentation in an early successional tree (Elaeocarpus grandis). Heredity, 93, 610-618.
52. Rousset F (2003) Inferences from spatial population genetics. In: Handbook of Statistical Genetics (eds Balding DJ, Bishop M, Cannings C), pp. 681-712. John Wiley & Sons, New York.
53. Routledge RD (1979) Diversity indices: which ones are admissible? Journal of Theoretical Biology, 76, 503-515.
54. Sarrazin C, Bruckner M, Herrmann E et al. (2001) Quasispecies heterogeneity of the carboxy-terminal part of the E2 gene including the PePHD and sensitivity of hepatitis C virus 1b isolates to antiviral therapy. Virology, 289, 150-163.
55. Sugden A, Pennissi E (2000) Special issue. Bioinformatics for biodiversity. Science 289 (5488), 2305-2314.
56. Shannon CE (1948) A mathematical theory of communication. The Bell System Technical Journal, 27, 379-423, 623-656.
57. Shervais S, Zwick M (2003) Ordering genetic algorithm genomes with reconstructability analysis. International Journal of General Systems, 32, 491-502.
58. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
59. Vellend M (2005) Species diversity and genetic diversity: parallel processes and correlated patterns. American Naturalist, 166, 199-215.
60. Wang Y-M, Ray SC, Laeyendecker O, Ticehurst JR, Thomas DL (1998) Assessment of hepatitis C virus sequence complexity by electrophoretic mobilities of both single- and double-stranded DNAs. Journal of Clinical Microbiology, 36, 2982-2989.
61. Wang T, Su Y-J, Li X-Y et al. (2004) Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data. Hereditas, 140, 8-17.
62. Watve MG, Gangal RM (1996) Problems in measuring bacterial diversity and a possible solution. Applied and Environmental Microbiology, 62, 4299-4301.
63. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
64. Whitlock MC (1992) Temporal fluctuations in demographic parameters and the genetic variance among populations. Evolution, 46, 608-615.
65. Whittaker RH (1972) Evolution and the measurement of species diversity. Taxon, 21, 213-251.
66. Zeeberg B (2002) Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes. Genome Research, 12, 944-955.