The West Pacific diversity hotspot as a source or sink for new species? Population genetic insights from the Indo-Pacific parrotfish Scarus rubroviolaceus

Molecular Ecology

Volumn 20, Issue 2, 2011, Pages 219-234

  Fitzpatrick, J M ^a   Carlon, D B ^a   Lippe, C ^a,c   Robertson, D R ^b  

^a UNIVERSITY OF HAWAII   (United States)

^b SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^c BD Diagnostics   (Canada)

Author keywords

gene flow; IMa; microsatellites; peripatric speciation; stepwise mutation model

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; GENE FLOW; GENETIC VARIABILITY; GENETICS; GENOTYPE; INDIAN OCEAN; METAGENOMICS; MUTATION; PACIFIC OCEAN; PERCIFORMES; PHYLOGENY; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION MIGRATION; SPECIES DIFFERENTIATION;

ANIMAL MIGRATION; ANIMALS; GENE FLOW; GENETIC SPECIATION; GENETIC VARIATION; GENOTYPE; INDIAN OCEAN; METAGENOMICS; MICROSATELLITE REPEATS; MUTATION; PACIFIC OCEAN; PERCIFORMES; PHYLOGENY; POPULATION DENSITY; POPULATION DYNAMICS;

SCARIDAE; SCARUS RUBROVIOLACEUS;

EID: 78651310372     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04942.x     Document Type: Article

References (62)

1. Alfaro ME, Brock CD, Banbury BL, Wainwright PC, (2009) Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes? BMC Evolutionary Biology, 9, 255.
2. Avise JC, (2004) Molecular Markers, Natural History, and Evolution, 2nd edn. Sinauer Associates, Sunderland, MA.
3. Barber PH, Erdmann MV, Palumbi SR, (2006) Comparative phylogeography of three codistributed stomatopods: origins and timing of regional lineage diversification in the coral triangle. Evolution, 60, 1825-1839.
4. Bay LK, Choat JH, van Herwerden L, Robertson DR, (2004) High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past? Marine Biology, 144, 757-767.
5. Beaumont MA, Rannala B, (2004) The Bayesian revolution in genetics. Nature Reviews Genetics, 5, 251-261.
6. Bellwood DR, Choat JH, (1990) A functional analysis of grazing in parrot fishes (family Scaridae): the ecological implications. Environmental Biology of Fishes, 28, 189-214.
7. Benzie JAH, (1999) Genetic structure of coral reef organisms: ghosts of dispersal past. American Zoologist, 39, 131-145.
8. Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR, (2001) Phylogeography of the trumpetfishes (Aulostomus): ring species complex on a global scale. Evolution, 55, 1029-1039.
9. Briggs JC, (1999) Coincident biogeographic patterns: Indo-West Pacific Ocean. Evolution, 53, 326-335.
10. Briggs JC, (2003) Marine centres of origin as evolutionary engines. Journal of Biogeography, 30, 1-18.
11. Carlon DB, Lippe C, (2007) Isolation and characterization of 17 new microsatellite markers for the ember parrotfish Scarus rubroviolaceus, and cross-amplification in four other parrotfish species. Molecular Ecology Notes, 7, 613-616.
12. Chen LS, (1999) Ontogenetic development in post settlement scarids (Pisces: Scaridae). PhD Dissertation, James Cook University, Townsville, Australia.
13. Colborn J, Crabtree RE, Shaklee JB, Pfeiler E, Bowen BW, (2001) The evolutionary enigma of bonefishes (Albula spp.): cryptic species and ancient separations in a globally distributed shorefish. Evolution, 55, 807-820.
14. Crandall ED, Frey MA, Grosberg RK, Barber PH, (2008) Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods. Molecular Ecology, 17, 611-626.
15. Dieringer D, Schlotterer C, (2003) MICROSATELLITE ANALYSER (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167-169.
16. Dyer RJ, (2009) Genetic Studio: a suite of programs for spatial analysis of genetic-marker data. Molecular Ecology Resources, 9, 110-113.
17. Dyer RJ, Nason JD, (2004) Population graphs: the graph theoretic shape of genetic structure. Molecular Ecology, 13, 1713-1727.
18. Ekman S, (1953) Zoogeography of the Sea. Sidgwick and Jackson, London.
19. Ellegren H, (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445.
20. Estoup A, Cornuet J-M, (1999) Microsatellites: evolution and applications. In: Microsatellite Evolution: Inferences from Population Data (eds, Goldstein DB, Schlotterer C,), 49-64. Oxford University Press, Oxford.
21. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
22. Excoffier L, Hofer T, Foll M, (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
23. Foll M, Gaggiotti O, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977.
24. Frey MA, Vermeij GJ, (2008) Molecular phylogenies and historical biogeography of a circumtropical group of gastropods (Genus: Nerita): implications for regional diversity patterns in the marine tropics. Molecular Phylogenetics and Evolution, 48, 1067-1086.
25. Hewitt G, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
26. Hey J, Nielsen R, (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D-persimilis. Genetics, 167, 747-760.
27. Hey J, Nielsen R, (2007) Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United States of America, 104, 2785-2790.
28. Hobbs JPA, Frisch AJ, Allen GR, Van Herwerden L, (2009) Marine hybrid hotspot at Indo-Pacific biogeographic border. Biology Letters, 5, 258-261.
29. Howard KG, (2008) Community structure, life history, and movement patterns of parrotfishes: large protogynous fishery species. PhD Dissertation, University of Hawaii, Honolulu, HI, USA.
30. Hughes TP, Bellwood DR, Connolly SR, (2002) Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecology Letters, 5, 775-784.
31. Jakobsson M, Rosenberg NA, (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801.
32. Jokiel P, Martinelli FJ, (1992) The vortex model of coral reef biogeography. Journal of Biogeography, 19, 449-458.
33. Jones AG, Rosenqvist G, Berglund A, Avise JC, (1999) Clustered microsatellite mutations in the pipefish Syngnathus typhle. Genetics, 152, 1057.
34. Kazancioglu E, Near TJ, Hanel R, Wainwright PC, (2009) Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae). Proceedings Biological Sciences/The Royal Society, 276, 3439-3446.
35. Lambeck K, Esat TM, Potter EK, (2002) Links between climate and sea levels for the past three million years. Nature, 419, 199-206.
36. Leopoldino AM, Pena SDJ, (2003) The mutational spectrum of human autosomal tetranucleotide microsatellites. Human Mutation, 21, 71-79.
37. Lessios HA, Robertson DR, (2006) Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier. Proceedings. Biological Sciences/The Royal Society, 273, 2201-2208.
38. Lessios HA, Kessing BD, Pearse JS, (2001) Population structure and speciation in tropical seas: global phylogeography of the sea urchin Diadema. Evolution, 55, 955-975.
39. Lessios HA, Kane J, Robertson DR, (2003) Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans. Evolution, 57, 2026-2036.
40. Losos JB, Glor RE, (2003) Phylogenetic comparative methods and the geography of speciation. Trends in Ecology & Evolution, 18, 220-227.
41. Malay MCMD, Paulay G, (2009) Peripatric speciation drives diversification and distributional pattern of reef hermit crabs (Decapoda: Diogenidae: Calcinus). Evolution, 64, 632-664.
42. Meyer CP, Geller JB, Paulay G, (2005) Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods. Evolution, 59, 113-125.
43. Mora C, Chittaro PM, Sale PF, Kritzer JP, Ludsin SA, (2003) Patterns and processes in reef fish diversity. Nature, 421, 933-936.
44. Nielsen R, (1997) A likelihood approach to populations samples of microsatellite alleles. Genetics, 146, 711-716.
45. Nielsen R, PalsbÃll PJ, (1999) Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size. Molecular Phylogenetics and Evolution, 11, 477-484.
46. Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D, (2009) Population genomics of marine fishes: identifying adaptive variation in space and time. Molecular Ecology, 18, 3128-3150.
47. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P, (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
48. Parenti P, Randall JE, (2000) An annotated checklist of the species of the labroid fish families Labridae and Scaridae. Ichthyological Bulletin, 68, 1-97.
49. Pavey SA, Nielsen JL, Hamon TR, (2009) Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka). Evolution, 64, 1773-1783.
50. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
51. Randall JE, (1998) Shore Fishes of Hawaii. University of Hawaii Press, Honolulu, HI.
52. Robertson DR, Allen GR, (2008) Shorefishes of the tropical Eastern Pacific online information system.
53. Robertson DR, Grove JS, McCosker JE, (2004) Tropical transpacific shore fishes. Pacific Science, 58, 507-565.
54. Rosenberg NA, (2004) DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
55. Steinberg EK, Lindner KR, Gallea J, Maxwell A, Meng J, Allendorf FW, (2002) Rates and patterns of microsatellite mutations in pink salmon. Molecular Biology and Evolution, 19, 1198.
56. Storey J, Storey JD, Tibshirani R, (2003) Statistical significance for genome-wide experiments. Proceedings of the National Academy of Sciences of the United States of America, 100, 9440-9445.
57. Strasburg JL, Rieseberg LH, (2010) How robust are"Isolation with Migration" analyses to violations of the IM model? A simulation study. Molecular Biology and Evolution, 27, 297-310.
58. Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA, (2002) Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution, 56, 961-971.
59. Williams ST, Duda TF, (2008) Did tectonic activity stimulate Oligo-Miocene speciation in the Indo-West Pacific? Evolution, 62, 1618-1634.
60. Williams ST, Reid DG, (2004) Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina. Evolution, 58, 2227-2251.
61. Williams ST, Jara J, Gomez E, Knowlton N, (2002) The marine Indo-West Pacific break: contrasting the resolving power of mitochondrial and nuclear genes. Integrative and Comparative Biology, 42, 941-952.
62. Woodland DJ, (1983) Zoogeography of the Siganidae (Pisces): an interpretation of distribution and richness patterns. Bulletin of Marine Science, 33, 713-717.