Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

Molecular Ecology

Volumn 25, Issue 1, 2016, Pages 260-268

  McGee, Matthew D ^a,b   Neches, Russell Y ^c   Seehausen, Ole ^a,b  

^a UNIVERSITY OF BERN   (Switzerland)

^b SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

adaptation; adaptive radiation; population genomics; speciation

Indexed keywords

ANIMAL; CICHLID; CLASSIFICATION; EVOLUTION; GENETICS; LAKE; MITOCHONDRIAL GENOME; PHENOTYPE; SPECIES DIFFERENTIATION; SYMPATRY;

ANIMALS; BIOLOGICAL EVOLUTION; CICHLIDS; GENETIC SPECIATION; GENOME, MITOCHONDRIAL; LAKES; PHENOTYPE; SYMPATRY;

EID: 84954057914     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13463     Document Type: Article

References (58)

1. Arnegard ME, McGee MD, Matthews B, et al. (2014) Genetics of ecological divergence during speciation. Nature, 511, 307-311
2. Azuma Y, Kumazawa Y, Miya M, Mabuchi K, Nishida M, (2008) Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evolutionary Biology, 8, 215
3. Bezault E, Mwaiko S, Seehausen O, (2011) Population genomic tests of models of adaptive radiation in Lake Victoria region cichlid fish. Evolution, 65, 3381-3397
4. Bierne N, Roze D, Welch JJ, (2013) Pervasive selection or is it...? Why are FST outliers sometimes so frequent? Molecular Ecology, 22, 2061-2064
5. Bouckaert R, Heled J, Kühnert D, et al. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10, e1003537
6. Brawand D, Wagner CE, Li YI, et al. (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513, 375-381
7. Butlin R, Debelle A, Kerth C, et al. (2012) What do we need to know about speciation? Trends in Ecology & Evolution, 27, 27-39
8. Carneiro M, Blanco-Aguiar JA, Villafuerte R, Ferrand N, Nachman MW, (2010) Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes. Evolution, 64, 3443-3460
9. Charlesworth B, (1998) Measures of divergence between populations and the effect of forces that reduce variability. Molecular Biology and Evolution, 15, 538-543
10. Coyne JA, Orr HA, (2004) Speciation (Vol. 37). Sinauer Associates, Sunderland, Massachusetts
11. Cruickshank TE, Hahn MW, (2014) Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology, 23, 3133-3157
12. Darriba D, Taboada GL, Doallo R, Posada D, (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772
13. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797
14. Ellegren H, Smeds L, Burri R, et al. (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491, 756-760
15. Estrada C, Jiggins CD, (2002) Patterns of pollen feeding and habitat preference among Heliconius species. Ecological Entomology, 27, 448-456
16. Feder JL, Egan SP, Nosil P, (2012) The genomics of speciation-with-gene-flow. Trends in Genetics, 28, 342-350
17. Friedman M, Keck BP, Dornburg A, et al. (2013) Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proceedings of the Royal Society B: Biological Sciences, 280, 20131733
18. Fryer G, Iles TD, (1972) The Cichlid fishes of the great lakes of Africa: their biology and evolution
19. Gagnaire PA, Pavey SA, Normandeau E, Bernatchez L, (2013) The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by rad sequencing. Evolution, 67, 2483-2497
20. Gavrilets S, (2004) Fitness Landscapes and the Origin of Species (MPB-41). Princeton University Press, Princeton, New Jersey
21. Genner MJ, Seehausen O, Lunt DH, et al. (2007) Age of cichlids: new dates for ancient lake fish radiations. Molecular Biology and Evolution, 24, 1269-1282
22. Greenwood PH, (1981) Towards a Phyletic Classification of the 'Genus' Haplochromis (Pisces, Cichlidae) and Related Taxa Part I. Bulletin of the British Museum (Natural History). Zoology, 35, 265-322
23. Hahn C, Bachmann L, Chevreux B, (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Research, 41, e129
24. Harr B, (2006) Genomic islands of differentiation between house mouse subspecies. Genome Research, 16, 730-737
25. Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP, (2006) A single amino acid mutation contributes to adaptive beach mouse color pattern. Science, 313, 101-104
26. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ, (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+ C)-biased genomes. Nature Methods, 6, 291-295
27. Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359
28. Lehmann T, Diabate A, (2008) The molecular forms of Anopheles gambiae: a phenotypic perspective. Infection, Genetics and Evolution, 8, 737-746
29. Li H, Handsaker B, Wysoker A, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079
30. Martin SH, Dasmahapatra KK, Nadeau NJ, et al. (2013) Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research, 23, 1817-1828
31. McKenna A, Hanna M, Banks E, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303
32. Noor MA, Bennett SM, (2009) Islands of speciation or mirages in the desert?; Examining the role of restricted recombination in maintaining species. Heredity, 103, 439-444
33. Noor MA, Feder JL, (2006) Speciation genetics: evolving approaches. Nature Reviews Genetics, 7, 851-861
34. Nosil P, (2012) Ecological Speciation. Oxford University Press, Oxford
35. Perez F, Granger BE, (2007) IPython: a system for interactive scientific computing. Computing in Science & Engineering, 9, 21-29
36. Rambaut A, Drummond A, (2003) Tracer: a program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes
37. Renaut S, Grassa CJ, Yeaman S, et al. (2013) Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nature Communications, 4, 1827
38. Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB, (2014) A role for migration-linked genes and genomic islands in divergence of a songbird. Molecular Ecology, 23, 4757-4769
39. Salzburger W, Van Bocxlaer B, Cohen AS, (2014) Ecology and evolution of the African Great Lakes and their faunas. Annual Review of Ecology, Evolution, and Systematics, 45, 519-545
40. Schluter D, Conte GL, (2009) Genetics and ecological speciation. Proceedings of the National Academy of Sciences, USA, 106, 9955-9962
41. Schwarzer J, Swartz ER, Vreven E, et al. (2012) Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution. Proceedings of the Royal Society of London B: Biological Sciences, 279, 4389-4398
42. Schwarzer J, Lamboj A, Langen K, Misof B, Schliewen UK, (2015) Phylogeny and age of chromidotilapiine cichlids (Teleostei: Cichlidae). Hydrobiologia, 748, 185-199
43. Seehausen O, (2002) Patterns in fish radiation are compatible with Pleistocene desiccation of Lake Victoria and 14 600 year history for its cichlid species flock. Proceedings of the Royal Society of London B: Biological Sciences, 269, 491-497
44. Seehausen O, (2006) African cichlid fish: a model system in adaptive radiation research. Proceedings of the Royal Society of London B: Biological Sciences, 273, 1987-1998
45. Seehausen O, (2015) Process and pattern in cichlid radiations-inferences for understanding unusually high rates of evolutionary diversification. New Phytologist, 207, 304-312
46. Seehausen O, Lippitsch E, Bouton N, Heleen Z, (1998) Mbipi, the rock-dwelling cichlids of Lake Victoria: description of three new genera and fifteen new species (Teleostei). Ichthyological Exploration of Freshwaters, 9, 129-228
47. Seehausen O, Butlin RK, Keller I, et al. (2014) Genomics and the origin of species. Nature Reviews Genetics, 15, 176-192
48. Snoeks J, (1994) Haplochromines (Teleostei, Cichlidae) of Lake Kivu (East Africa)
49. Stelkens RB, Seehausen O, (2009) Genetic distance between species predicts novel trait expression in their hybrids. Evolution, 63, 884-897
50. Stelkens RB, Schmid C, Seehausen O, (2015) Hybrid breakdown in cichlid fish. PLoS ONE, 10, e0127207
51. Turner TL, Hahn MW, Nuzhdin SV, (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3, e285
52. Turner TL, Stewart AD, Fields AT, Rice WR, Tarone AM, (2011) Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genetics, 7, e1001336
53. Via S, West J, (2008) The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Molecular Ecology, 17, 4334-4345
54. Wagner CE, Harmon LJ, Seehausen O, (2012) Ecological opportunity and sexual selection together predict adaptive radiation. Nature, 487, 366-369
55. Wainwright PC, Richard BA, (1995) Predicting patterns of prey use from morphology of fishes. Environmental Biology of Fishes, 44, 97-113
56. Williams EE, (1972) The origin of faunas. Evolution of lizard congeners in a complex island fauna: a trial analysis. Evolutionary Biology, 6, 47-89
57. Wu CI, (2001) The genic view of the process of speciation. Journal of Evolutionary Biology, 14, 851-865
58. Wu CI, Ting CT, (2004) Genes and speciation. Nature Reviews Genetics, 5, 114-122