Standardizing methods to address clonality in population studies

Molecular Ecology

Volumn 16, Issue 24, 2007, Pages 5115-5139

  Arnaud Haond, S ^a   Duarte, C M ^b   Alberto, F ^a   Serrao E A ^a  

^a UNIVERSITY OF ALGARVE   (Portugal)

^b INSTITUTO MEDITERRÁNEO DE ESTUDIOS AVANZADOS   (Spain)

Author keywords

Clonal diversity; Clonal size; Clonal subrange; Clonality; Methods; Molecular markers; Power law; Sampling design; Spatial autocorrelation; Species richness

Indexed keywords

BIOLOGICAL MARKER;

CLASSIFICATION; COMPUTER PROGRAM; GENETICS; GENOTYPE; METHODOLOGY; PLANT; POPULATION DYNAMICS; POPULATION GENETICS; REVIEW; STANDARD;

BIOLOGICAL MARKERS; GENETICS, POPULATION; GENOTYPE; PLANTS; POPULATION DYNAMICS; SOFTWARE;

ANIMALIA; CYMODOCEA NODOSA; POSIDONIA OCEANICA;

EID: 37249022873     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03535.x     Document Type: Review

References (74)

1. Alberto F, Correia L, Arnaud-Haond S, Billot C, Duarte CM, Serrão EA (2003a) New microsatellites markers for the endemic Mediterranean seagrass, Posidonia oceanica. Molecular Ecology Notes, 3, 253 255.
2. Alberto F, Correia L, Billot C, Duarte CM, Serrao EA (2003b) Isolation and characterization of microsatellite markers for the seagrass, Cymodocea nodosa. Molecular Ecology Notes, 3, 397 399.
3. Alberto F, Gouveia L, Arnaud-Haond S, Pérens-Lloréns JL, Duarte CM, Serrão EA (2005) Spatial genetic structure, neighbourhood size and clonal subrange in seagrass (Cymodocea nodosa) populations. Molecular Ecology, 14, 2669 2681.
4. Anderson JB, Kohn LM (1995) Clonality in soilborne, plant-pathogenic fungi. Annual Review of Phytopathology, 33, 369 391.
5. Arnaud-Haond S, Alberto F, Teixeira S, Procaccini G, Serrao EA, Duarte CM (2005) Assessing genetic diversity in clonal organisms: low diversity or low resolution? Combining power and cost-efficiency in selecting markers. Journal of Heredity, 96, 434 440.
6. Arnaud-Haond S, Belkhir K (2007) genclone 1.0: a new program to analyse genetics data on clonal organisms. Molecular Ecology Notes, 7, 15 17.
7. Arnaud-Haond S, Diaz Almela E, Teixeira S, Alberto F, Duarte CM, Serrao EA (2007) Vicariance patterns in the Mediterranean sea: East-West cleavage and low dispersal in the endemic seagrass Posidonia oceanica. Journal of Biogeography, 34, 963 976.
8. Ayre DJ, Hughes TP (2000) Genotypic diversity and gene flow in brooding and spawning corals along the Great Barrier Reef, Australia. Evolution, 54, 1590 1605.
9. Bastidas C, Benzie JAH, Uthicke S, Fabricius KE (2001) Genetic differentiation among populations of a broadcast spawning soft coral, Sinularia flexibilis, on the Great Barrier Reef. Marine Biology, 138, 517 525.
10. Charpentier A (2001) Consequences of clonal growth for plant mating. Evolutionary Ecology, 15, 521 530.
11. Cheplick GP (1997) Responses to severe competitive stress in a clonal plant: differences between genotypes. Oikos, 79, 581 591.
12. Chung MY, Nason JD, Chung MG (2004) Implications of clonal structure for effective population size and genetic drift in a rare terrestrial orchid, Cremastra appendiculata. Conservation Biology, 18, 1515 1524.
13. Cywinska A, Hebert PDN (2002) Origins of clonal diversity in the hypervariable asexual ostracode Cypridopsis vidua. Journal of Evolutionary Biology, 15, 134 145.
14. Diaz-Almela E, Arnaud-Haond S, van de Vliet MS et al. Feed-backs between genetic structure and perturbation-driven decline in seagrass (Posidonia oceanica) Meadows Conservation Genetics, doi:.
15. Dorken ME, Eckert CG (2001) Severely reduced sexual reproduction in northern populations of a clonal plant, Decodon verticillatus (Lythraceae). Journal of Ecology, 89, 339 350.
16. Douhovnikoff V, Dodd RS (2003) Intra-clonal variation and a similarity threshold for identification of clones: application to Salix exigua using AFLP molecular markers. Theoretical and Applied Genetics, 106, 1307 1315.
17. Ellstrand NC, Roose ML (1987) Patterns of genotypic diversity in clonal plant-species. American Journal of Botany, 74, 123 131.
18. Epperson BK, Li TQ (1997) Gene dispersal and spatial genetic structure. Evolution, 51, 672 681.
19. Fager EW (1972) Diversity: a sampling study. American Naturalist 106, 293 310.
20. Freeland JR, Noble LR, Okamura B (2000) Genetic diversity of North American populations of Cristatella mucedo, inferred from microsatellite and mitochondrial DNA. Molecular Ecology, 9, 1375 1389.
21. Gini C (1912) Variabilità e mutabilità. In : Studi Economico-Giuridici Facolta de Giurisprundenza dell' Universita di Cagliari, A., Vol III, parte II.
22. Gregorius H-R (2005) Testing for clonal propagation. Heredity, 94, 173 179.
23. van Groenendael J, de Kroon H (1990) Clonal Growth in Plants: Regulation and Function. SPB Academic Publishers, The Hague, The Netherlands.
24. Halkett F, Plantegenest M, Prunier-Leterme N, Mieuzet L, Delmotte F, Simon JC (2005a) Admixed sexual and facultatively asexual aphid lineages at mating sites. Molecular Ecology, 14, 325 336.
25. Halkett F, Simon JC, Balloux F (2005b) Tackling the population genetics of clonal and partially clonal organisms. Trends in Ecology & Evolution, 20, 194 201.
26. Hammerli A, Reusch TBH (2003) Genetic neighbourhood of clone structures in eelgrass meadows quantified by spatial autocorrelation of microsatellite markers. Heredity, 91, 448 455.
27. Hangelbroek HH, Ouborg NJ, Santamaria L, Schwenk K (2002) Clonal diversity and structure within a population of the pondweed Potamogeton pectinatus foraged by Bewick's swans. Molecular Ecology, 11, 2137 2150.
28. Harada Y, Kawano S, Iwasa Y (1997) Probability of clonal identity: inferring the relative success of sexual versus clonal reproduction from spatial genetic patterns. Journal of Ecology, 85, 591 600.
29. Harper JL (1977) Population Biology of Plants. Academic Press, London.
30. Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology, 54, 427 432.
31. Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52, 577 586.
32. Kapralov MV (2004) Genotypic variation in populations of the clonal plant Saxifraga cernua in the central and peripheral regions of the species range. Russian Journal of Ecology, 35, 413 416.
33. Klekowski EJ (2003) Plant clonality, mutation, diplontic selection and mutational meltdown. Biological Journal of the Linnean Society, 79, 61 67.
34. Le Goff-Vitry MC, Pybus OG, Rogers AD (2004) Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences. Molecular Ecology, 13, 537 549.
35. Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Molecular Ecology, 11, 2445 2449.
36. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany, 82, 1420 1425.
37. Lovett-Doust L (1981) Population dynamics and local specialization in a clonal perrenial (Ranunculus repens). I. The dynamics of ramets in contrasting habitats. Journal of Ecology, 69, 743 755.
38. Loxdale HD, Lushai G (2003) Rapid changes in clonal lines: the death of a 'sacred cow'. Biological Journal of the Linnean Society, 79, 3 16.
39. Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792 794.
40. Murawski DA, Hamrick JL (1990) Local genetic and clonal structure in the tropical terrestrial bromeliad, Aechmea magdalenae. American Journal of Botany, 77, 1201 1208.
41. Nagamitsu T, Ogawa M, Ishida K, Tanouchi H (2004) Clonal diversity, genetic structure, and mode of recruitment in a Prunus ssiori population established after volcanic eruptions. Plant Ecology, 174, 1 10.
42. Olsen JL, Stam WT, Coyer JA et al 2004) North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Molecular Ecology, 13, 1923 1941.
43. Parker ED Jr. (1979) Ecological implications of clonal diversity in parthenogenetic morphospecies. American Zoologist, 19, 753 762.
44. Parks JC, Werth CR (1993) A study of spatial features of clones in a population of Bracken fern, Pteridium aquilinum (Dennstaedtiaceae). American Journal of Botany, 80, 537 544.
45. Peakall R, Smouse P (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
46. Peet R (1974) The measurement of species diversity. Annual Review of Ecology and Systematics, 5, 285 307.
47. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology, 12, 844 855.
48. Pielou EC (1966) Shannon's formulae as a measure of species diversity: its use and misuse. American Naturalist, 100, 463 465.
49. Pielou EC (1969) An Introduction to Mathematical Ecology. Wiley-Interscience, New-York.
50. Pielou EC (1975) Ecological diversity. New York, USA Y, SaumitouLaprade P, Petit D, Vernet P, Epplen JT (1996) Genotypic diversity revealed by allozymes and oligonucleotide DNA fingerprinting in French populations of the aquatic macrophyte, Sparganium erectum. Molecular Ecology, 5, 251 258.
51. Reusch TBH (2001) New markers - old questions: population genetics of seagrasses. Marine Ecology - Progress Series, 211, 261 274.
52. Reusch TBH, Hukriede W, Stam WT, Olsen JL (1999) Differentiating between clonal growth and limited gene flow using spatial autocorrelation of microsatellites. Heredity, 83, 120 126.
53. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genetical Research, 67, 175 185.
54. Rousset F (2000) Genetic differentiation between individuals. Journal of Evolutionary Biology, 13, 58 62.
55. Rozenfeld AF, Arnaud-Haond S, Hernández-García E et al 2007) Spectrum of genetic diversity and networks of clonal populations Journal of the Royal Society Interface.
56. Schroeder M (1991) Fractals, Chaos, Power Laws: Minutes from an Infinite Paradise. W.H. Freeman, New York.
57. Simpson EH (1949) Measurements of diversity. Nature, 163, 688.
58. Sintes T, Marba N, Duarte CM, Kendrick GA (2005) Nonlinear processes in seagrass colonisation explained by simple clonal growth rules. Oikos, 108, 165 175.
59. Smith B, Wilson JB (1996) A consumer's guide to evenness measures Oikos, 76, 70 82.
60. Sokal RR, Rohlf FJ (1995) Biometry. W.H. Freeman, New York.
61. StatSoft I (2001) statistica (Data Analysis Software System), Version 6. http://www.statsoft.com.
62. Stenberg P, Lundmark M, Saura A (2003) mlgsim: a program for detecting clones using a simulation approach. Molecular Ecology Notes, 3, 329 331.
63. Stoddart JA (1983) A genotypic diversity measure. Journal of Heredity, 74, 489 490.
64. Stoddart JA, Taylor JF (1988) Genotypic diversity - estimation and prediction in samples. Genetics, 118, 705 711.
65. Suehs CM, Affre L, Medail F (2004) Invasion dynamics of two alien Carpobrotus (Aizoaceae) taxa on a Mediterranean island: I. Genetic diversity and introgression. Heredity, 92, 31 40.
66. Taylor DJ, Foighil DO (2000) Transglobal comparisons of nuclear and mitochondrial genetic structure in a marine polyploid clam (Lasaea, Lasaeidae). Heredity, 84, 321 330.
67. Tibayrenc M, Ayala FJ (2002) The clonal theory of parasitic protozoa: 12 years on. Trends in Parasitology, 18, 405 410.
68. Tibayrenc M, Kjellberg F, Ayala F (1990) A clonal theory of oarasitic protozoa: the population structures of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas, and Trypanosoma and their medical and taxonomical consequences. Proceedings of the National Academy of Sciences, USA, 87, 2414 2418.
69. Ueda HR, Hayashi S, Matsuyama S et al 2004) Universality and flexibility in gene expression from bacteria to human. Proceedings of the National Academy of Sciences, USA, 101, 3765 3769.
70. Uthike S, Benzie JAH, Ballment E (1998) Genetic structure of fissiparous populations of Holothuria (Halodeima) atra on the Great Barrier Reef. Marine Biology, 132, 141 151.
71. Van der Hulst RGM, Mes THM, Falque M, Stam P, Den Nijs JCM, Bachmann K (2003) Genetic structure of a population sample of apomictic dandelions. Heredity, 90, 326 335.
72. Vidondo B, Prairie YT, Blanco JM, Duarte CM (1997) Some aspects of the analysis of size spectra in aquatic ecology. Limnology and Oceanography, 42, 184 192.
73. Washington HG (1984) Diversity, biotic and similarity indices. A review with special relevance to aquatic ecosystems. Water Research, 18, 653 694.
74. Young AG, Hill JH, Murray BG, Peakall R (2002) Breeding system, genetic diversity and clonal structure in the sub-alpine forb Rutidosis leiolepis F. Muell. (Asteraceae). Biological Conservation, 106, 71 78.