Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

Genetics and Molecular Biology

Volumn 30, Issue 4, 2007, Pages 1125-1134

  Ochieng, Joel W ^a,d   Steane, Dorothy A ^b   Ladiges, Pauline Y ^c   Baverstock, Peter R ^a   Henry, Robert J ^a   Shepherd, Mervyn ^a  

^a SOUTHERN CROSS UNIVERSITY   (Australia)

^b UNIVERSITY OF TASMANIA   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF NAIROBI   (Kenya)

Author keywords

Eucalypts; Homoplasy; Incongruence; Microsatellite phylogeny; Paraphyletic

Indexed keywords

INTERNAL TRANSCRIBED SPACER; SPACER DNA;

ARTICLE; CONTROLLED STUDY; GENE TRANSFER; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC VARIABILITY; GENOME SIZE; GENUS; HOMOPLASY; MICROSATELLITE MARKER; MOLECULAR PHYLOGENY; MONOPHYLY; MORPHOLOGICAL TRAIT; MUTATION RATE; MYRTACEAE; NONHUMAN; PARAPHYLY; PLANT GENETICS; SIMPLE SEQUENCE REPEAT; TAXON;

BROSIMUM RUBESCENS; CORYMBIA (ANGIOSPERM); MYRTACEAE;

EID: 37649021769     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572007000600016     Document Type: Article

References (65)

1. Asante KS, Brophy JJ, Doran JC, Goldsack RJ, Hibbert DB and Larmour JS (2001) A comparative study of the seedling leaf oils of the spotted gums: Species 'of the Corymbia (Myrtaceae), section Politaria. Aust J Bot 49:55-66.
2. Avise JC (2000) The History and Formation of Species. Harvard University Press, Cambridge, Massachusets, 439 pp.,
3. Avise JC, Ankney CD and Nelson WS (1990) Mitochondrial gene trees and the evolutionary relationship of mallard and black ducks. Evolution 44:1109-1119.
4. Bayly MJ and Ladiges PY (2007) Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae). Mol Phylogenet Evol 44:346-356.
5. Brooker MIH (2000) A new classification of the genus Eucalyptus L'Her. (Myrtaceae). Aust Syst Bot 13:79-148.
6. Bruford MW and Wyne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939-943.
7. Carr DJ, Car SGM, Hyland BPM, Wilson PG and Ladiges PY (2002) Stockwellia quadrifida (Myrtaceae), a new genus and species in the eucalypt group. Biol J Linn Soc 139:415-421.
8. Cavalli-Sforza LL and Edwards WF (1967) Phylogenetic analysis: Models and estimation procedures. Evolution 21:550-570.
9. Crisp M, Cook L and Steane DA (2004) Radiation of the Australian flora: What can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities? Phil Trans R Soc B 359:1551-1571.
10. Demastes JW and Remsen Jr. JC (1994) The genus Caryonthraustes ( Cardinalinae) is not monophyletic. Wilson Bull 106:733-738.
11. Dumolin-Lapegue S, Demesure B, Fineschi S, Le Corre V and Petit RJ (1997) Phylogeographic structure of white oaks throughout the European continent. Genetics 146:1475-1487.
12. Ellegren H, Primmer CR and Sheldon BC (1995) Microsatellite evolution: Directionality or bias in locus selection. Nat Genet 11:360-362.
13. Estoup A, Jarne P and Cornuet J-M (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11: 1591-1604.
14. Feldman MW, Bergman A, Pollock DD and Goldstein DB (1997) Microsatellite genetic distances with range constraints: Analytical description and problems of estimation. Genetics 29:207-216.
15. Felsenstein J (1995) PHYLIP: Phylogeny Inference Package. University of Washington, Seattle.
16. Forbes SH, Hogg JT, Buchanan FC, Crawford AM and Allendorf FW (1995) Microsatellite evolution in congeneric mammals: Domestic and Bighorn sheep. Mol Biol Evol 12:1106-1113.
17. Garza JC and Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res 6:211-217.
18. Goldstein DB and Pollock DD (1997) Launching microsatellites: A review of mutation processes and methods of phylogenetic inference. Heredity 88:335-342.
19. Goldstein DB, Roemer G, Smith D, Reich DE, Bergman A and Wayne R (1999) The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151:797-801.
20. Goldstein DB, Ruiz LA, Cavalli-Sforza LL and Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463-471.
21. GoudetJ (2001) A computer program to calculate F-statistics. Heredity 86:485-456.
22. Hill KD and Johnson LAS (1995) Systematic studies in the eucalypts 7. A revision of the bloodwoods, genus Corymbia (Myrtaceae). Telopea 6:185-504.
23. Johnson LAS and Briggs BG (1984) Myrtales and Myrtaceae - A phylogenetic analysis. Ann Mo Bot Gard 71:700-756.
24. Jones ME, Stokoe RL, Cross MJ, Scott LJ, Maguire TL and Shepherd M (2001) Isolation of microsatellite loci from spotted gum (Corymbia variegata), and cross-species amplification in Corymbia and Eucalyptus. Mol Ecol Notes 1:276-278.
25. Kalinowski S T (2005) Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity 94:33-36.
26. Kimura M and Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725-738.
27. Kimura M and Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 75:2868-2872.
28. King R (2004) Spatial structure and population genetic variation in a Eucalypt species complex. PhD Thesis, Griffith University, Australia.
29. Ladiges PY, Udovicic F and Drinnan AN (1995) Eucalypt phylogeny - Molecules and morphology. Aust Syst Bot 8:483-497.
30. Ladiges PY, and Udovicic F (2000) Comment on a new classification of the Eucalypts. Aust Syst Bot 13:149-152.
31. Ladiges PY, Udovicic F and Nelson G (2003) Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae. J Biogeogr 30:989-998.
32. Lu Y (2001) Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae. Heredity 86:195-205.
33. Maddison WP (1997) Gene trees in species trees. Syst Biol 46:523-536.
34. McCracken KG and Sorenson MD (2005) Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)? Syst Biol 54:35-55.
35. McDonald MW, Butcher PA, Bell JC and Larmour JS (2000) Intra- and interspecific allozyme variation in eucalypts from the spotted gum group, Corymbia, section 'Politaria' (Myrtaceae). Aust Syst Bot 13:491-507.
36. McKinnon GE, Steane DA, Potts BM and Vaillancourt RE (1999) Incongruence between chloroplast and species phylogenies in Eucalyptus subgenus Monocalyptus (Myrtaceae). Am J Bot 86:1038-1046.
37. Moran GF and Brown AHD (1980) Temporal heterogeneity of outcrossing rates in alpine ash (Eucalyptus delegatensis R.T. Bak.). Theor Appl Genet 57:101-105.
38. Nei M (1972) Genetic distance between populations. Am Nat 106:283-292.
39. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
40. Ochieng JW, Henry RJ, Baverstock PR, Steane DA and Shepherd M (2007) Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs. Mol Phylogenet Evol 44:752-764.
41. Parra-O C, Bayly M, Udovicic F and Ladiges P (2006) ETS sequences support the monophyly of the eucalypt genus Corymbia (Myrtaceae). Taxon 55:653-663.
42. Peakall R, Gilmore S, Keys W, Morgante M and Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other Legume genera: Implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275-1267.
43. Petren KB, Grant R and Grant PR (1999) A phylogeny of Darwin's finches based on microsatellite DNA length variation. Proc R Soc London B 266:321-329.
44. Pollock DD, Bergman A, Feldman MW and Goldstein DB (1998) Microsatellite behaviour with range constraints: parameter estimation and improved distances for use in phylogenetic reconstruction. Theor Pop Biol 53:256-271.
45. Pryor LD and Johnson LAS (1971) A Classification of the Eucalypts. Australian National University Press, Canberra, 102 pp.
46. Richard M and Thorpe RS (2001) Can microsatellites be used to infer phylogenies? Evidence from population affinities of the western Canary Island lizard (Gallotia galloti). Mol Phylogenet Evol 20:351-360.
47. Ritz LR, Glowatzki-Mullis ML, MacHugh DE and Gaillard C (2000) Phylogenetic analysis of the tribe Bovini using microsatellites. Anim Genet 31, 178-185.
48. Rodrigo AG, Kelly-Borges M, Bergquist PR and PL Bergquist (1993) A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zeal J Bot 31:257-268.
49. Rubinstein DC, Amos W, Leggo J, Goodbum S, Jain S, Li S-H, Margolis RL, Ross CA and Ferguson-Smith MA (1995) Microsatellite evolution - Evidence for directionality and variation in rate between species. Nat Genet 10:337-343.
50. Ruzzante DE (1998) A comparison of several measures of generic distance and population structure with microsatellite data: Bias and sampling variance. Can J Fish Aquat Sci 55:1-14.
51. Shepherd M, Kasem S, Lee D and Henry R (2006) Construction of microsatellite genetic, linkage maps for Corymbia. Silvae Genet 55:228-238.
52. Southerton SG, Birt P and Ford HA (2004) Review of gene movement by bats and birds and its potential significance for eucalypt plantation forestry. Aust For 67:44-53.
53. Steane DA, McKinnon GE, Vaillancourt RE and Potts BM (1999) ITS sequence data resolves higher level relationships among the eucalypts. Mol Phylogenet Evol 12:215-223.
54. Steane DA, Nicolle D, McKinnon GE, Vaillancourt RE and Potts BM (2002) Higher-level relationships among the eucalypts are resolved by ITS-sequence data. Aust Syst Bot 15:49-62.
55. Streelman JT, Zardoya R, Meyer A and Karl SA (1998) Multilocus phylogeny of cichlid fishes (Pisces, Perciformes): Evolutionary comparison of microsatellite and single-copy nuclear loci. Mol Biol Evol 15:798-808.
56. Takahashi K, Terai Y, Nishida M and Okada N (2001) Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol 18:2057-2066.
57. Takezaki N and Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389-399.
58. Thamarus KA, Groom K, Murrel J, Byrne M and Moran GF (2002) A genetic linkage map for Eucalyptus globulus with candidate loci for wood, fibre, and floral traits. Theor Appl Genet 104:379-387.
59. Udovicic F and Ladiges PY (2000) Informativeness of nuclear and chloroplast DNA regions and the phylogeny of the eucalypts and related genera (Myrtaceae). Kew Bullet 55:633-645.
60. Udovicic F, McFadden GI and Ladiges PY (1995) Phylogeny of Eucalyptus and Angophora based on 5S rDNA spacer sequence data. Mol Phylogenet Evol 4:247-256.
61. Whittock S, Steane DA, Vaillancourt RE and Potts BM (2003) Molecular evidence shows that the tropical boxes (Eucalyptus subgenus Minutifructus) are over-ranked. Trans R Soc S Aust 127:27-32.
62. Whitton J, Rieseberg; LH and Ungerer MC (1997) Microsatellite loci are not conserved across the Asteraceae. Mol Biol Evol 14:204-209.
63. Wilson PG, O'Brien MM, Gadek PA and Quinn CJ (2001) Myrtaceae revisisted: A reassessment of infrafamilial groups. Am J Bot 88:2013-2025.
64. Zhu Y, Queller DC and Strassmann JE (2000) A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol 50:324-338.
65. Zink RM (2002) A new perspective on the evolutionary history of Darwin's finches. The Auk 119:864-871.