Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

Molecular Ecology Resources

Volumn 15, Issue 5, 2015, Pages 1031-1045

  Kemppainen, Petri ^a,b   Knight, Christopher G ^a   Sarma, Devojit K ^a,c   Hlaing, Thaung ^d   Prakash, Anil ^c   Maung Maung, Yan Naung ^d   Somboon, Pradya ^e   Mahanta, Jagadish ^c   Walton, Catherine ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b INSTITUTE OF VERTEBRATE BIOLOGY   (Czech Republic)

^c REGIONAL MEDICAL RESEARCH CENTRE   (India)

^d Department of Medical Research (Lower Myanmar) Medical Entomology Research Division   (Myanmar)

^e Faculty of Medicine Chiang Mai University   (Thailand)

Author keywords

Anopheles dirus; Anopheles gambiae; Chromosomal rearrangement; Graph theory; Landscape genomics; r package

Indexed keywords

ANOPHELES DIRUS; ANOPHELES GAMBIAE; GASTEROSTEUS ACULEATUS;

ANIMAL; ANOPHELES; BIOLOGY; CHROMOSOME INVERSION; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; EVALUATION STUDY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; MOLECULAR EVOLUTION; POPULATION GENETICS; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SMEGMAMORPHA;

ANIMALS; ANOPHELES; CHROMOSOME INVERSION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETICS, POPULATION; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SMEGMAMORPHA;

EID: 84938989827     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12369     Document Type: Article

References (61)

1. Andrew RL, Bernatchez L, Bonin A et al. (2013) A road map for molecular ecology. Molecular Ecology, 22, 2605-2626.
2. Ardlie KG, Kruglyak L, Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics, 3, 299-309.
3. Baimai V, Poopittayasataporn A, Kijchalao U (1988a) Cytological differences and chromosomal rearrangements in four members of the Anopheles dirus complex (Diptera: Culicidae). Genome, 30, 372-379.
4. Baimai V, Thu MM, Paing M (1988b) Distribution and chromosomal polymorphism of the malaria vector Anopheles dirus species D. The Southeast Asian Journal of Tropical Medicine and Public Health, 19, 661-665.
5. Barton NH (2011) Estimating linkage disequilibria. Heredity, 106, 205-206.
6. Barton NH, Briggs D, Eisen JA, Goldstein DB (2007) Evolution. Cold spring harbor laboratory press, Cold Spring Harbor, New York.
7. Bolshakov VN (2002) A comparative genomic analysis of two distant Diptera, the fruit fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae. Genome Research, 12, 57-66.
8. Colosimo PF, Hosemann KE, Balabhadra S et al. (2005) Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science, 307, 1928-1933.
9. Conrad DF, Jakobsson M, Coop G et al. (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics, 38, 1251-1260.
10. Corbett-Detig RB, Cardeno C, Langley CH (2012) Sequence-based detection and breakpoint assembly of polymorphic inversions. Genetics, 192, 131-137.
11. Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal, Complex Systems, 1695, http://cran.r-project.org/web/packages/igraph/citation.html.
12. Davey JW, Hohenlohe PA, Etter PD, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
13. Davey JW, Cezard T, Fuentes-Utrilla P et al. (2013) Special features of RAD Sequencing data: implications for genotyping. Molecular Ecology, 22, 3151-3164.
14. Excoffier L, Foll M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics (Oxford, England), 27, 1332-1334.
15. Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M (2013) Robust demographic inference from genomic and SNP data. PLoS Genetics, 9, e1003905.
16. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
17. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574-578.
18. Fisher CM, Foll M, Excoffier L, Heckel G (2011) Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Molecular Ecology, 20, 1450-1462.
19. Foote AD, Similä T, Víkingsson GA, Stevick PT (2009) Movement, site fidelity and connectivity in a top marine predator, the killer whale. Evolutionary Ecology, 24, 803-814.
20. Gaggiotti OE, Bekkevold D, Jørgensen HBH et al. (2009) Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study. Evolution, 63, 2939-2951.
21. Gray MM, Granka JM, Bustamante CD et al. (2009) Linkage disequilibrium and demographic history of wild and domestic canids. Genetics, 181, 1493-1505.
22. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. TAG. Theoretical and Applied Genetics. Theoretische und angewandte Genetik, 38, 226-231.
23. Hoffmann AA, Rieseberg LH (2008) Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation? Annual Review of Ecology, Evolution, and Systematics, 39, 21-42.
24. Hohenlohe PA, Bassham S, Currey M, Cresko WA (2012) Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 367, 395-408.
25. International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
26. Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics (Oxford, England), 27, 3070-3071.
27. Jones FC, Grabherr MG, Chan YF et al. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484, 55-61.
28. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Research, 12, 656-664.
29. Kim S, Plagnol V, Hu TT et al. (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genetics, 39, 1151-1155.
30. Kim Y, Feng S, Zeng Z-B (2008) Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains. Genetic Epidemiology, 32, 301-312.
31. Kirkpatrick M, Barton N (2006) Chromosome inversions, local adaptation and speciation. Genetics, 173, 419-434.
32. Knight CG, Pinney JW (2009) Making the right connections: biological networks in the light of evolution. BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, 31, 1080-1090.
33. Koch E, Ristroph M, Kirkpatrick M (2013) Long range linkage disequilibrium across the human genome. PLoS One, 8, e80754.
34. Kumasaka N, Nakamura Y, Kamatani N (2010) The textile plot: a new linkage disequilibrium display of multiple-single nucleotide polymorphism genotype data. PLoS One, 5, e10207.
35. Lawson DJ, Hellenthal G, Myers S, Falush D (2012) Inference of population structure using dense haplotype data. PLoS Genetics, 8, e1002453.
36. Leskovec J, Lang KJ, Dasgupta A, Mahoney MW (2009) Community structure in large networks: natural cluster sizes and the absence of large well-defined clusters. Internet Mathematics, 6, 29-123.
37. Lowry DB, Willis JH (2010) A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biology, 8, e1000500.
38. Maniatis N (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proceedings of the National Academy of Sciences of the USA, 99, 2228-2233.
39. Marbach D, Prill RJ, Schaffter T et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the USA, 107, 6286-6291.
40. Mason O, Verwoerd M (2007) Graph theory and networks in Biology. IET Systems Biology, 1, 89-119.
41. Morgan K, Linton Y-M, Somboon P et al. (2010) Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia. Molecular Ecology, 19, 2269-2285.
42. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA (2013) Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology, 22, 2841-2847.
43. Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 69, 026113.
44. Noor MAF, Bennett SM (2009) Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity, 103, 439-444.
45. Obsomer V, Defourny P, Coosemans M (2012) Predicted distribution of major malaria vectors belonging to the Anopheles dirus complex in Asia: ecological niche and environmental influences. PLoS One, 7, e50475.
46. Poopittayasataporn A, Baimai V (1995) Polytene chromosome relationships of five species of the Anopheles dirus complex in Thailand. Genome, 38, 426-434.
47. R Core Team (2014) A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
48. Ralph P, Coop G (2013) The geography of recent genetic ancestry across Europe. PLoS Biology, 11, e1001555.
49. Rieseberg LH (2001) Chromosomal rearrangements and speciation. Trends in Ecology & Evolution, 16, 351-358.
50. Sabeti PC, Varilly P, Fry B et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature, 449, 913-918.
51. Sarma DK, Prakash A, O'Loughlin SM et al. (2012) Genetic population structure of the malaria vector Anopheles baimaii in north-east India using mitochondrial DNA. Malaria Journal, 11, 76.
52. Schumer M, Cui R, Powell D et al. (2014) High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. eLife. doi: 10.7554/eLife.02535.
53. Seeb JE, Carvalho G, Hauser L et al. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11, 1-8.
54. Sinka ME, Bangs MJ, Manguin S et al. (2011) The dominant Anopheles vectors of human malaria in the Asia-Pacific region: occurrence data, distribution maps and bionomic précis. Parasites & Vectors, 4, 89.
55. Slate J, Pemberton JM (2007) Admixture and patterns of linkage disequilibrium in a free-living vertebrate population. Journal of Evolutionary Biology, 20, 1415-1427.
56. Slatkin M (2008) Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics, 9, 477-485.
57. Tang X, Szinay D, Lang C et al. (2008) Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics, 180, 1319-1328.
58. Via S (2011) Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 367, 451-460.
59. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biology, 4, e72.
60. Warnes G, Gorjanc WCFG, Leisch F, Man M (2013) The genetics package. R package version 1.3.8.1. Available from http://CRAN.R-project.org/package=genetics.
61. Wilson JF, Goldstein DB (2000) Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population. American Journal of Human Genetics, 67, 926-935.