Applicability of RAD-tag genotyping for interfamilial comparisons: Empirical data from two cetaceans

Molecular Ecology Resources

Volumn 14, Issue 3, 2014, Pages 597-605

  Viricel, Amélia ^a   Pante, Eric ^a   Dabin, Willy ^b   Simon Bouhet, Benoit ^a  

^a French National Centre for Scientific Research   (France)

^b La Rochelle Université   (France)

Author keywords

Delphinidae; Genomics; Interfamilial divergence; Phocoenidae; Phylogenetics; RAD sequencing

Indexed keywords

ANIMAL; CETACEA; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION STUDY; FEMALE; GENETICS; GENOTYPE; MALE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

ANIMALS; BASE SEQUENCE; CETACEA; EVOLUTION, MOLECULAR; FEMALE; GENOTYPE; MALE; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

EID: 84898448634     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12206     Document Type: Article

References (59)

1. Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
2. Altschul SF, Madden TL, Schäffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
3. Amaral AR, Silva MC, Möller LM, Beheregaray LB, Coelho MM (2010) Anonymous nuclear markers for cetacean species. Conservation Genetics, 11, 1143-1146.
4. Arnason U, Gullberg A, Janke A (2004) Mitogenomic analysis provide new insight into cetacean origin and evolution. Gene, 333, 27-34.
5. Baxter SW, Davey JW, Johnston JS et al. (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a nonmodel organism. PLoS ONE, 6, e19315.
6. Bergey CM, Pozzi L, Disotell TR, Burrell AS (2013) A new method for genome-wide marker development and genotyping holds great promise for molecular primatology. International Journal of Primatology, 34, 303-314.
7. Bininda-Emonds ORP (2007) Fast genes and slow clades: comparative rates of molecular evolution in mammals. Evolutionary Bioinformatics, 3, 59-85.
8. Blüthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D (2005) Biological profiling of gene groups utilizing gene ontology. Genome Informatics, 16, 106-115.
9. Britten RJ (1986) Rates of DNA sequence evolution differ between taxonomic groups. Science, 231, 1393-1398.
10. Cariou M, Duret L, Charlat S (2013) Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecology and Evolution, 3, 846-852.
11. Carstens B, Lemmon AR, Lemmon EM (2012) The promises and pitfalls of next-generation sequencing data in phylogeography. Systematic Biology, 61, 713-715.
12. Catchen JM, Amores A, Hohenlohe P, CreskoW, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda), 1, 171-182.
13. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.
14. Chan AH, Jenkins PA, Song YS (2012) Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, 8, e1003090.
15. Conesa A, Götz S (2008) Blast2go: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, Article ID 619832.
16. Conesa A, Götz S, García-Gömez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
17. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML (2013) Special features of RAD sequencing data: implications for genotyping. Molecular Ecology, 22, 3151-3164.
18. Eaton DAR, Ree RH (2013) Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology, 62, 689-706.
19. Emerson KJ, Merz CR, Catchen JM et al. (2010) Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America, 107, 16196-16200.
20. Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology, 61, 717-726.
21. Fordyce RE (1980) Whale evolution and Oligocene Southern Ocean environments. Palaeogeography, Palaeoclimatology, Palaeoecology, 31, 319-336.
22. Gagnaire PA, Normandeau E, Pavey SA, Bernatchez L (2013) Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Molecular Ecology, 22, 3036-3048.
23. Götz S, Garciá-Gómez JM, Terol J et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 36, 3420-3435.
24. Götz S, Arnold R, Sebastián-León P et al. (2011) B2G-FAR, a species-centered GO annotation repository. Bioinformatics, 27, 919-924.
25. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11 (Suppl 1), 117-122.
26. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.
27. Jones JC, Fan S, Franchini P, Schartl M, Meyer A (2013) The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Molecular Ecology, 22, 2986-3001.
28. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059-3066.
29. Keller I, Wagner CE, Greuter L et al. (2013) Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Molecular Ecology, 22, 2848-2863.
30. Kingston SE, Rosel PE (2004) Genetic differentiation among recently diverged delphinid taxa determined using AFLP markers. Journal of Heredity, 95, 1-10.
31. Kingston SE, Adams LD, Rosel PE (2009) Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae). BMC Evolutionary Biology, 9, 245.
32. Kocher TD, Thomas WK, Meyer A et al. (1989) Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 86, 6196-6200.
33. Lemmon EM, Lemmon AR (2013) High-throughput genomic data in systematics and phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 44, 19.1-19.23.
34. Lemmon AR, Emme SA, Lemmon EM (2012) Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61, 727-744.
35. Lexer C, Mangili S, Bossolini E et al. (2013) 'Next generation' biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography, 40, 1013-1022.
36. Martin AP, Palumbi SR (1993) Body size, metabolic rate, generation time, and the molecular clock. Proceedings of the National Academy of Sciences of the United States of America, 90, 4087-4091.
37. McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC (2012) Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Research, 22, 746-754.
38. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66, 526-538.
39. McGowen MR, Spaulding M, Gatesy J (2009) Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Molecular Phylogenetics and Evolution, 53, 891-906.
40. McGowen MR, Grossman LI, Wildman DE (2012) Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proceedings of the Royal Society B-Biological Sciences, 279, 3643-3651.
41. Nadeau NJ, Martin SH, Kozak KM et al. (2013) Genome-wide patterns of divergence and gene flow across a buttery radiation. Molecular Ecology, 22, 814-826.
42. Palumbi S, Martin A, Romano S, McMillan W, Stice L, Grabowski G (1991) The Simple Fool's Guide to PCR. version 2.0. Tech. Rep., University of Hawaii, Honolulu.
43. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
44. Perrin W, Würzig B, Thewissen J, (eds) (2009) Encyclopedia of Marine Mammals, 2nd edn. Academic Press, San Diego.
45. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and nonmodel species. PLoS ONE, 7, e37135.
46. R Development Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
47. Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM (2013) Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Molecular Ecology, 22, 2953-2970.
48. Rosel PE, Dizon AE, Heyning JE (1994) Genetic-analysis of sympatric morphotypes of common dolphins (genus Delphinus). Marine Biology, 119, 159-167.
49. Rosel PE, Tiedemann R, Walton M (1999) Genetic evidence for limited trans-Atlantic movements of the harbor porpoise Phocoena phocoena. Marine Biology, 133, 583-591.
50. Rubin BER, Ree RH, Moreau CS (2012) Inferring phylogenies from RAD sequence data. PLoS ONE, 7, e33394.
51. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics, 13, 3.
52. Stapley J, Reger J, Feulner PDG et al. (2010) Adaptation genomics: the next generation. Trends in Ecology & Evolution, 25, 705-712.
53. Steeman ME, Hebsgaard MB, Fordyce RE, et al. (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573-585.
54. Stölting KN, Nipper R, Lindtke D et al. (2013) Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Molecular Ecology, 22, 842-855.
55. Viricel A, Rosel PE (2012) Evaluating the utility of cox1 for cetacean species identification. Marine Mammal Science, 28, 37-62.
56. Vollmer NL, Rosel PE (2012) Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterization of 153 single nucleotide polymorphisms and 53 genotyping assays. Molecular Ecology Resources, 12, 1124-1132.
57. Vollmer NL, Viricel A, Wilcox L, Moore MK, Rosel PE (2011) The occurrence of mtDNA heteroplasmy in multiple cetacean species. Current Genetics, 57, 115-131.
58. Wagner CE, Keller I, Wittwer S et al. (2013) Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22, 787-798.
59. Xiong Y, Brandley MC, Xu S, Zhou K, Yang G (2009) Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evolutionary Biology, 9, 20.