Minding the gap: Frequency of indels in mtDNA control region sequence data and influence on population genetic analyses

Molecular Ecology

Volumn 15, Issue 2, 2006, Pages 333-341

  Pearce, John M ^a,b  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^b U S GEOLOGICAL SURVEY   (United States)

Author keywords

Control region; Gap; Indel; mtDNA; Population genetics

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENE DELETION; GENETIC VARIABILITY; GENETICS; POPULATION GENETICS; REGULATOR GENE; TRANSPOSON; VERTEBRATE;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; DNA, MITOCHONDRIAL; GENETICS, POPULATION; LOCUS CONTROL REGION; MODELS, GENETIC; SEQUENCE DELETION; VARIATION (GENETICS); VERTEBRATES;

VERTEBRATA;

EID: 33645085602     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02781.x     Document Type: Article

References (74)

1. Balakrishnan CN Monfort SL Gaur A Singh L Sorenson MD 2003 Phylogeography and conservation genetics of Eld's deer (Cervus eldi) Molecular Ecology 12 1 10
2. Ballard JWO Whitlock MC 2004 The incomplete natural history of mitochondria Molecular Ecology 13 729 744
3. Benedict NG Oyler-McCance SJ Taylor SE Braun CE Quinn TW 2003 Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (C. u. phaios) subspecies of sage-grouse using mitochondrial control-region sequence data Conservation Genetics 4 301 310
4. Bulgin NL Gibbs HL Vickery P Baker AJ 2003 Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus) Molecular Ecology 12 831 844
5. Buroker NE Brown JR Gilbert TA et al. 1990 Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model Genetics 124 157 163
6. Caicedo AL Schaal BA 2004 Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene Molecular Ecology 13 1871 1882
7. Chiang TY Schaal BA 1999 Phylogeography of North American populations of the moss species Hylocomium splendens based on the nucleotide sequence of internal transcribed spacer 2 of nuclear ribosomal DNA Molecular Ecology 8 1037 1042
8. Clegg MT Gaut BS Learn GH Morton BR 1994 Rates and patterns of chloroplast DNA evolution Proceedings of the National Academy of Sciences, USA 91 6795 6801
9. Dalport W Ferguson JWH Bloomer P 2002 Characterization and evolution of the mitochondrial DNA control region in hornbills (Bucerotiformes) Journal of Molecular Evolution 54 794 806
10. Drew RE Hallett JG Aubry KB et al. 2003 Conservation genetics of the fisher (Martes pennanti) based on mitochondrial DNA sequencing Molecular Ecology 12 51 62
11. Ericson PG Johansson US Parsons TJ 2000 Major divisions in Oscines revealed by insertions in the nuclear gene c-myc: a novel gene in avian phylogenetics Auk 117 1069 1078
12. Escorza-Trevino S Dizon AE 2000 Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses Molecular Ecology 9 1049 1060
13. Excoffier L Smouse PE Quattro JM 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data Genetics 131 479 491
14. Farris JS 1989 The retention index and the rescale consistency index Cladistics 5 417 419
15. Garrick RC Sands CJ Rowell DM et al. 2004 Phylogeography recapitulates topography: very fine-scale local endemism of a saproxylic 'giant' springtail at Tallaganda in the Great Dividing Range of southeast Australia Molecular Ecology 13 3329 3344
16. Gaut BS Muse SV Clegg MT 1993 Relative rates of nucleotide substitution in the chloroplast genome Molecular Phylogenetics and Evolution 7 89 96
17. Gielly L Taberlet P 1994 The use of chloroplast DNA to resolve plant phylogenies: non-coding vs. rbcL sequences Molecular Biology and Evolution 7 769 777
18. Godoy JA Negro JJ Hiraldo F Donázar JA 2004 Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L.) as revealed by mitochondrial DNA Molecular Ecology 13 371 390
19. Gottelli D Marino J Sillero-Zubiri C Funk SM 2004 The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis) Molecular Ecology 13 2275 2286
20. Gregory TR 2004 Insertion-deletion biases and the evolution of genome size Gene 324 15 34
21. Griswold CK Baker AJ 2002 Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration Evolution 56 143 153
22. Haavie J Sætre GP Moum T 2000 Discrepancies in population differentiation at microsatellites, mitochondrial DNA and plumage colour in the pied flycatcher - inferring evolutionary processes Molecular Ecology 9 1137 1148
23. Hamilton MB Braverman JM Soria-Hernanz DF 2003 Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae Molecular Biology and Evolution 20 1710 1721
24. Hardy OJ Charbonnel N Fréville H Heuertz M 2003 Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation Genetics 163 1467 1482
25. Higgins DG Thompson JD Gibson TJ 1996 Using clustal for multiple sequence alignments Methods in Enzymology 266 383 402
26. Hirota T Hirohata T Mashima H Satoh T Obara Y 2004 Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences Molecular Ecology 13 3275 3282
27. Huang S Chiang YC Schaal BA Chou CH Chiang TY 2001 Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan Molecular Ecology 10 2669 2681
28. Ingvarsson PK Ribstein S Taylor DR 2003 Molecular evolution of insertions and deletions in the chloroplast genome of Silene Molecular Biology and Evolution 20 1737 1740
29. Jerry DR Braverstock PR 1998 Consequences of catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata Molecular Ecology 7 1003 1013
30. Johnson JA Toepfer JE Dunn PO 2003 Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens Molecular Ecology 12 3335 3347
31. Keeney DB Huepel MR Hueter RE Heist EJ 2005 Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea Molecular Ecology 14 1911 1923
32. King TL Eackles MS Gjetvaj B Hoeh WR 1999 Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): conservation implications of range discontinuity Molecular Ecology 8 S65 S78
33. Kluge AG Farris JS 1969 Quantitative phyletics and the evolution of anurans Systematic Zoology 18 1 32
34. Kontula T Väinölä R 2001 Post-glacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio Molecular Ecology 10 1983 2002
35. Krebs RA 2004 Combining paternally and maternally inherited mitochondrial DNA for analysis of population structure in mussels Molecular Ecology 13 1701 1705
36. Kumar S Tamura K Jakobsen IB Nei M 2001 mega: molecular revolutionary genetics analysis software Bioinformatics 17 1244 1245
37. Ludwig A May B Debus L Jenneckens I 2000 Heteroplasmy in the mtDNA, control region of sturgeon (Acipenser, Huso, and Scaphirhynchus) Genetics 156 1933 1947
38. Ludwig A Con giu L Pitra C et al. 2003 Nonconcordant evolutionary history of maternal and paternal lineages in Adriatic sturgeon Molecular Ecology 12 3253 3264
39. Lundy CJ Rico C Hewitt GM 2000 Temporal and spatial genetic variation in spawning grounds of European hake (Merluccius merluccius) in the Bay of Biscay Molecular Ecology 9 2067 2079
40. Maddison D Maddison W 2000 macclade 40: Analysis of Phylogeny and Character Evolution Sinauer Associates Sunderland, Massachusetts
41. Norusis MJ 2001 SPSS Professional Statistics V11.0 SPSS Chicago, Illinois
42. Nyakaana S Arctander P 1999 Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow Molecular Ecology 8 1105 1115
43. Patriana A Hatch SA Friesen VL 2002 Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA Conservation Genetics 3 335 340
44. Pearce RL Wood JJ Artukhin Birt TP Damus M Friesen VL 2002 Mitochondrial DNA suggests high gene flow in ancient murrelets Condor 104 84 91
45. Perez-Tris J Bensch S Carbonell R Helbig AJ Telleria JL 2004 Historical diversification of migration patterns in a passerine bird Evolution 58 1819 1832
46. Pope LC Estoup A Moritz C 2000 Phylogeography and population structure of an ecotonal marsupial, Bettongia tropica, determined using mtDNA and microsatellites Molecular Ecology 9 2041 2053
47. Prychitko TM Moore WS 2003 Alignment and phylogenetic analysis of β-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron Molecular Biology and Evolution 20 762 771
48. Rambaut A 1996 se-al: Sequence Alignment Editor Computer program available at
49. Randi E Lucchini V Christensen MF et al. 2000 Mitochondrial DNA variability in Italian and East European wolves: detecting the consequences of small population size and hybridization Conservation Biology 14 464 473
50. Ross TK 1999 Phylogeography and conservation genetics of the Iowa Pleistocene snail Molecular Ecology 8 1363 1373
51. Rozas J Rozas R 1999 ) dnasp version 3.1 An integrated programme for molecular population genetics and molecular evolution analysis Bioinformatics 15 174 175
52. Ruokonen M Aarvak T Madsen J 2005 Colonization history of the high-arctic pink-footed goose Anser brachyrhynchus Molecular Ecology 14 171 178
53. Salgueiro P Coelho MM Palmeirim JM Ruedi M 2004 Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum) Molecular Ecology 13 3357 3366
54. Saunders MA Edwards SV 2000 Dynamics and phylogenetic implications of mtDNA control region sequences in New World Jays (Aves: Corvidae) Journal of Molecular Evolution 51 97 109
55. Schneider S Roessli D Excoffier L 2000 arlequin, Version 200: A software for population genetics data analysis Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva Switzerland
56. Schultheis AS Weigt LA Hendricks AC 2002 Gene flow, dispersal, and nested clade analysis among populations of the stonefly Peltoperla tarteri in the southern Appalachians Molecular Ecology 11 317 327
57. Shanker K Ramadevi J Choudhury BC Singh L 2004 Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory Molecular Ecology 13 1899 1909
58. Shaw AJ 2000 Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae) Molecular Ecology 9 595 608
59. Simmons MP Ochoterena H 2000 Gaps as characters in sequence-based phylogenetic analyses Systematic Biology 49 369 381
60. Simmons MP Ochoterena H Carr TG 2001 Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analysis Systematic Biology 50 454 462
61. Smith CT Nelson RJ Wood CC Koop BF 2001 Glacial biogeography of North American coho salmon (Oncorhynchus kisutch) Molecular Ecology 10 2775 2785
62. Sundstrom H Webster MT Ellegren H 2003 Is the rate of insertion and deletion mutation male biased? Molecular evolutionary analysis of avian and primate sex chromosome sequences Genetics 164 259 268
63. Swofford DL 2002 paup *: Phylogenetic Analysis Using Parsimony (*and Other Methods) version 4 Sinauer Associates
64. Tani N Tsumura Y Sato H 2003 Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period Molecular Ecology 12 859 868
65. Taylor MS Ponting CP Copley RR 2004 Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes Genome Research 14 555 566
66. Teske PR Cherry MI Matthee CA 2003 Population genetics of the endangered Knysna seahorse, Hippocampus capensis Molecular Ecology 12 1703 1715
67. Tiedemann R Paulus KB Scheer M et al. 2004 Mitochondrial DNA and microsatellite variation in the eider duck (Somateria mollissima) indicate stepwise postglacial colonization of Europe and limited current long-distance dispersal Molecular Ecology 13 1481 1494
68. Vernesi C Pecchioli E Caramelli D Tiedemann R Randi E 2002 The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy, with reference to the mitochondrial DNA phylogeography of Europe Molecular Ecology 11 1285 1297
69. Weber JL David D Heil J Fan Y Zhao C Marth G 2002 Human diallelic insertion/deletion polymorphisms American Journal of Human Genetics 71 854 862
70. Weiss S Antunes A Schlötterer C Alexandrino P 2000 Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-Pleistocene recolonization of northern Europe Molecular Ecology 9 691 698
71. Weiss S Persat H Eppe R Schlötterer C Uiblein F 2002 Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region Molecular Ecology 11 1393 1407
72. Wright SI Lauga B Charlesworth D 2003 Subdivision and haplotype structure in natural populations of Arabidopsis lyrata Molecular Ecology 12 1247 1263
73. Zhang D Hewitt GM 2003 Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects Molecular Ecology 12 563 584
74. Zink RM Barrowclough GF Atwood JL Blackwell-Rago RC 2000 Genetics, taxonomy, and conservation of the threatened California gnatcatcher Conservation Biology 14 1394 1405