Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus)

Heredity

Volumn 108, Issue 5, 2012, Pages 531-536

  Campos, R ^a,b   Storz, J F ^c   Ferrand, N ^a,b  

^a CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^b UNIVERSITY OF PORTO   (Portugal)

^c UNIVERSITY OF NEBRASKA   (United States)

Author keywords

copy number polymorphism; European rabbit; gene duplication; haemoglobin; hybridization

Indexed keywords

HEMOGLOBIN A;

AMINO ACID; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENE EXPRESSION; GENOMICS; GEOGRAPHICAL VARIATION; HYBRID; HYBRIDIZATION; LAGOMORPH; PLEISTOCENE; POLYMORPHISM; POPULATION STRUCTURE;

ALLELE; ANIMAL; ARTICLE; CLASSIFICATION; COPY NUMBER VARIATION; FEMALE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; MALE; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; RABBIT;

ALLELES; ANIMALS; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC VARIATION; HEMOGLOBIN A; MALE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; POLYMORPHISM, GENETIC; RABBITS;

EUROPE;

MAMMALIA; ORYCTOLAGUS CUNICULUS;

EID: 84860015344     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2011.118     Document Type: Article

References (50)

1. Bandelt H-J, Forster P, Röhl A (1999). Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48. (Pubitemid 29024937)
2. Barton NH, Hewitt GM (1985). Analysis of hybrid zones. Annu Rev Ecol Syst 16: 113-148.
3. Biju-Duval C, Ennafaa H, Dennebouy N, Monnerot M, Mignotte F, Soriguer RC et al. (1991). Mitochondrial DNA evolution in lagomorphs: origin of systematic heteroplasmy and organization of diversity in european rabbits. J Mol Evol 33: 92-102.
4. Bradley RD, Bull JJ, Johson AD, Hillis DM (1993). Origin of a novel allele in a mammalian hybrid zone. Proc Natl Acad Sci USA 90: 8939-8941. (Pubitemid 23306426)
5. Branco M, Ferrand N, Monnerot M (2000). Phylogeography of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula inferred from RFLP analysis of the cytochrome b gene. Heredity 85: 307-317. (Pubitemid 32122093)
6. Branco M, Ferrand N, Monnerot M, Templeton AR (2002). Postglacial dispersal of the European rabbit (Oryctolagus cuniculus) on the Iberian Peninsula reconstructed from nested clade and mismatch analyses of mitochondrial DNA genetic variation. Evolution 56: 792-803. (Pubitemid 34519790)
7. Bruen TC, Philippe H, Bryant D (2006). A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
8. Campos R, Branco M, Weiss S, Ferrand N (2007). Patterns of hemoglobin polymorphism [a-globin (HBA) and b-globin (HBB)] across the contact zone of two distinct phylogeographic lineages of the European rabbit (Oryctolagus cuniculus).. In: Weiss S, Ferrand N. (eds). Phylogeography of European Refugia. Springer: Netherlands. pp 237-255.
9. Campos R, Storz JF, Ferrand N (2008). Evidence for contrasting modes of selection at interacting globin genes in the European rabbit. Heredity 100: 602-609. (Pubitemid 351733272)
10. Carneiro M, Afonso S, Geraldes A, Garreau H, Bolet G, Boucher S et al. (2011). The genetic structure of domestic rabbits. Mol Biol Evol 28: 1801-1816.
11. Cheng JF, Hardison RC (1988). The rabbit a-like globin gene cluster is polymorphic both in the sizes of BamHI fragments and in the numbers of duplicated sets of genes. Mol Biol Evol 5: 486-498.
12. Cheng JF, Raid L, Hardison R (1986). Isolation and nucleotide sequence of the rabbit globin gene cluster cx-a1-ca. Absence of a pair of a-globin genes evolving in concert. J Biol Chem 261: 839-848. (Pubitemid 16161750)
13. Cheng JF, Raid L, Hardison R (1987). Block duplication of a z-z-a-y gene set in the rabbit a-like globin gene cluster. J Biol Chem 262: 5414-5421.
14. Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW (2006). Evolution of mammalian gene families. PLoS ONE 1: e85.
15. Excoffier L, Laval G, Schneider S (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
16. Excoffier L, Slatkin M (1995). Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12: 921-927.
17. Ferrand N, Azevedo M, Mougel F (2000). A diallelic short tandem repeat, (CCCCG) 4 or 5, located in intron 1 of rabbit a-globin gene. Anim Genet 31: 74.
18. Ferrand N, Branco M (2007). The evolutionary history of the European rabbit (Oryctolagus cuniculus): major patterns of population differentiation and geographic expansion inferred from protein polymorphism.. In: Weiss S, Ferrand N. (eds). Phylogeography of European Refugia. Springer: Netherlands. pp 207-235.
19. Fonseca A (2006) Análise da origem e dispersaõdas populações de coelho-bravo (Oryctolagus cuniculus) nos Arquipélagos dos Açores, Madeira e Canárias, através da utilizaçaõde marcadores gené ticos nucleares e de DNA mitocondrial. PhD Thesis, University of Açores.
20. Geraldes A, Carneiro M, Delibes-Mateos M, Villafuerte R, Nachman MW, Ferrand N (2008). Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian peninsula. Mol Ecol 17: 4489-4499.
21. Geraldes A, Ferrand N, Nachman MW (2006). Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 173: 919-933. (Pubitemid 43945907)
22. Geraldes A, Rogel-Gaillard C, Ferrand N (2005). High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene. Anim Genet 36: 349-351. (Pubitemid 41615474)
23. Godinho R, Mendonca B, Crespo EG, Ferrand N (2006). Genealogy of the nuclear betafibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone. Heredity 96: 4454-4463.
24. Hahn MW, Demuth JP, Han S-G (2007). Accelerated rate of gene gain and loss in primates. Genetics 177: 1941-1949. (Pubitemid 350277083)
25. Hardison R, Krane D, Vandenbergh D, Cheng JF, Mansberger J, Taddie J et al. (1991). Sequence and comparative analysis of the rabbit a-like globin gene cluster reveals a rapid mode of evolution in a G+C-rich region of mammalian genomes. J Mol Biol 222: 233-249. (Pubitemid 121004004)
26. Higgs DR (2001). Molecular mechanisms of a-thalassemia.. In: Steinberg MH, Forget BG, Higgs DR, Nagel RL (eds). Disorders of Hemoglobin: Genetics, Pathophysiology and Clinical management. Cambridge University Press: Cambridge. pp 405-430.
27. Hoffman SMG, Brown WM (1995). The molecular mechanism underlying the 'rare allele phenomenon' in a subspecific hybrid zone of the California field mouse, Peromyscus californicus. J Mol Evol 41: 1165-1169. (Pubitemid 26020094)
28. Hoffmann FG, Gorr TA, Storz JF, Opazo JC (2010). Lineage-specific patterns of functional diversification in the a-and b-globin gene families of tetrapod vertebrates. Mol Biol Evol 27: 1126-1138.
29. Hoffmann FG, Opazo JC, Storz JF (2008a). Rapid rates of lineage-specific gene duplication and deletion in the a-globin gene family. Mol Biol Evol 25: 591-602. (Pubitemid 351301915)
30. Hoffmann FG, Opazo JC, Storz JF (2008b). New genes originated via multiple recombinational pathways in the b-globin gene family of rodents. Mol Biol Evol 25: 2589-2600.
31. Hudson RR (1987). Estimating the recombination parameter of a finite population model without selection. Genet Res 50: 245-250. (Pubitemid 18042123)
32. Hudson RR, Kaplan NL (1985). Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164. (Pubitemid 16248827)
33. Librado P, Rozas J (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
34. Nei M (1987). Molecular Evolutionary Genetics. Columbia University Press: New York.
35. Opazo JC, Hoffmann FG, Storz JF (2008a). Differential loss of embryonic globin genes during the radiation of placental mammals. Proc Natl Acad Sci USA 105: 12950-12955.
36. Opazo JC, Hoffmann FG, Storz JF (2008b). Genomic evidence for independent origins of beta-like globin genes in monotremes and therian mammals. Proc Natl Acad Sci USA 105: 1590-1595. (Pubitemid 351346559)
37. Opazo JC, Sloan AM, Campbell KL, Storz JF (2009). Origin and ascendancy of a chimeric fusion gene: the beta/delta-globin gene of paenungulate mammals. Mol Biol Evol 26: 1469-1478.
38. Runck AM, Moriyama H, Storz JF (2009). Evolution of duplicated b-globin genes and the structural basis of hemoglobin isoform differentiation in Mus. Mol Biol Evol 26: 2521-2532.
39. Runck AM, Weber RE, Fago A, Storz JF (2010). Evolutionary and functional properties of a two-locus b-globin polymorphism in Indian house mice. Genetics 184: 1121-1131.
40. Schilthuizen M, Gittenberger E (1994). Parallel evolution of an sAat 'hybrizyme' in hybrid zones in Albinaria hippolyti (Boettger). Heredity 73: 244-248. (Pubitemid 2137941)
41. Schilthuizen M, Hoekstra RF, Gittenberger E (1999). Selective increase of a rare haplotype in a land snail hybrid zone. Proc R Soc Lond B7 266: 2181-2185. (Pubitemid 29532899)
42. Schilthuizen M, Hoekstra RF, Gittenberger E (2004). Hybridization, rare alleles and adaptive radiation. Trends Ecol Evol 19: 404-405.
43. Storz JF, Baze M, Waite JL, Hoffmann FG, Opazo JC, Hayes JP (2007). Complex signatures of selection and gene conversion in the duplicated globin genes of house mice. Genetics 177: 481-500.
44. Storz JF, Hoffmann FG, Opazo JC, Moriyama H (2008). Adaptive functional divergence among triplicated a-globin genes in rodents. Genetics 178: 1623-1638.
45. Storz JF, Runck AM, Moriyama H, Weber RE, Fago A (2010). Genetic differences in hemoglobin function between highland and lowland deer mice. J Exp Biol 213: 2565-2574.
46. Storz JF, Runck AM, Sabatino SJ, Kelly JK, Ferrand N, Moriyama H et al. (2009). Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proc Natl Acad Sci USA 106: 14450-14455.
47. Tajima F (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460. (Pubitemid 14247444)
48. Watterson GA (1975). On the number of segregating sites. Theor Popul Biol 7: 256-276.
49. Woodruff DS (1989). Genetic anomalies associated with Cerion hybrid zones: the origin and maintenance of new electrophoretic variants called hybrizymes. Biol J Linn Soc Lond 36: 281-294.
50. Zimmer EA, Martin SL, Beverley SM, Kan YW, Wilson AC (1980). Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc Natl Acad Sci USA 77: 2158-2162. (Pubitemid 10089617)