Population history, gene flow, and bottlenecks in island populations of a secondary seed disperser, the southern grey shrike (Lanius meridionalis koenigi)

Ecology and Evolution

Volumn 5, Issue 1, 2015, Pages 36-45

  Padilla, David P ^a,b   Spurgin, Lewis G ^a   Fairfield, Eleanor A ^a   Illera, Juan Carlos ^b,c   Richardson, David S ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b INSTITUTO DE PRODUCTOS NATURALES Y AGROBIOLOGÍA   (Spain)

^c UNIVERSITY OF OVIEDO   (Spain)

Author keywords

Canary Islands; Diplochory; Genetic structure; Microsatellites; MtDNA; Phylogeography

Indexed keywords

LANIIDAE; LANIUS MERIDIONALIS KOENIGI;

EID: 84920276544     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.1334     Document Type: Article

References (56)

1. Aljanabi, S. M., and I. Martinez. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25:4692-4693.
2. Avise, J. C. 2004. Molecular markers, natural history and evolution. Sinauer Associates, Sunderland, MA.beer.
3. Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl Acad. Sci. 98:4563-4568.
4. Beerli, P. 2009. How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use. Popul. Genet. Anim. Conserv. 17:42-79.
5. Beaumont, M. A. 2010. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41:379-406.
6. Cornuet, J. M., F. Santos, M. A. Beaumont, C. P. Robert, J. M. Marin, D. J. Balding, et al. 2008. Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics, 24:2713-2719.
7. Clement, M., D. Posada, and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9:1657-1659.
8. Cornuet, J. M., and G. Luikart. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001.
9. Cox, S. C., S. Carranza, and R. P. Brown. 2010. Divergence times and colonization of the Canary Islands by Gallotia lizards. Mol. Phylogenet. Evol. 56:747-757.
10. Crawford, N. G. 2010. SMOGD: software for the measurement of genetic diversity. Mol. Ecol. Res. 10:556-557.
11. Dawson, D. A., G. J. Horsburgh, C. Küpper, I. R. K. Stewart, A. D. Ball, K. L. Durrant, et al. 2010. New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility; as demonstrated for birds. Mol. Ecol. Res. 10:475-494.
12. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
13. Emerson, B. C. 2002. Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process. Mol. Ecol. 11:951-966.
14. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.
15. Excoffier, L., and H. E. L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10:564-567.
16. Garza, J. C., and E. G. Williamson. 2001. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 10:305-318.
17. Gonzalez, J., M. Wink, E. Garcia-del-Rey, and G. D. Castro. 2008. Evidence from DNA nucleotide sequences and ISSR profiles indicates paraphyly in subspecies of the Southern Grey Shrike (Lanius meridionalis). J. Ornithol. 149:495-506.
18. Goslee, S. C., and D. L. Urban. 2007. The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw. 22:1-19.
19. Griffiths, R., M. Double, K. Orr, and R. J. G. Dawson. 1998. A DNA test to sex most birds. Mol. Ecol. 7:1071-1075.
20. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
21. Higgins, S., R. Nathan, and M. Cain. 2003. Are long-distance dispersal events in plants usually caused by nonstandard means of dispersal? Ecology 84:1945-1956.
22. Illera, J. C., B. C. Emerson, and D. S. Richardson. 2007. Population history of Berthelot's pipit: colonization, gene flow and morphological divergence in Macaronesia. Mol. Ecol. 16:4599-4612.
23. Illera, J. C., J. C. Rando, D. S. Richardson, and B. C. Emerson. 2012. Age, origins and extinctions of the avifauna of Macaronesia: a synthesis of phylogenetic and fossil information. Quatern. Sci. Rev. 50:14-22.
24. IUCN (2004) 2004 IUCN Red list of threatened species. World Conservation Union, Cambridge, U.K.
25. Jombart, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403-1405.
26. Jost, L. 2008. GST and its relatives do not measure differentiation. Mol. Ecol. 17:4015-4026.
27. Juan, C., B. C. Emerson, P. Oromí, and G. M. Hewitt. 2000. Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands. Trends Ecol. Evol. 15:104-109.
28. Kenta, T., J. Gratten, N. S. Haigh, G. N. Hinten, J. Slate, R. K. Butlin, et al. 2008. Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method. Mol. Ecol. Notes 8:1230-1238.
29. Klassert, T. E., M. Hernández, F. Campos, O. Infante, T. Almeida, N. M. Suárez, et al. 2008. Mitochondrial DNA points to Lanius meridionalis as a polyphyletic species. Mol. Phylogenet. Evol. 47:1227-1231.
30. MacArthur, R. H., and E. O. Wilson. 1967. The theory of island biogeography. Princeton Univ Press, Princeton, NJ.
31. Marshall, T. C., J. Slate, L. E. B. Kruuk, and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7:639-655.
32. Martín, A., and J. A. Lorenzo. 2001. Aves del Archipiélago Canario. Francisco Lemus La Laguna, Tenerife.
33. Martinez, J. G., J. J. Soler, M. Soler, A. P. Møller, and T. Burke. 1999. Comparative population structure and gene flow of a brood parasite, the great spotted cuckoo (Clamator glandarius), and its primary host, the magpie (Pica pica). Evolution 53:269-278.
34. Mundy, N., and D. Woodruff. 1996. Polymorphic microsatellite markers in the loggerhead shrike Lanius ludovicianus isolated from a library enriched for CA repeats. Mol. Ecol. 5:811-813.
35. Nogales, M., J. Delgado, and F. M. Medina. 1998. Shrikes, lizards and Lycium intricatum (Solanaceae) fruits: a case of indirect seed dispersal on an oceanic island (Alegranza, Canary Islands). J. Ecol. 86:866-871.
36. Olsson, U., P. Alström, L. Svensson, M. Aliabadian, and P. Sundberg. 2010. The Lanius excubitor (Aves, Passeriformes) conundrum-Taxonomic dilemma when molecular and non-molecular data tell different stories. Mol. Phylogenet. Evol. 55:347-357.
37. Padilla, D. P., A. González-Castro, and M. Nogales. 2012. Significance and extent of secondary seed dispersal by predatory birds on oceanic islands: the case of the Canary archipelago. J. Ecol. 100:416-427.
38. Parker, P. G., A. A. Snow, M. D. Schug, G. C. Booton, and P. A. Fuerst. 1998. What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79:361-382.
39. Pinheiro, J., D. Bates, S. DebRoy, D. Sarkar, and R. D. C. Team 2013. nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-110.
40. Piry, S., G. Luikart, and J. M. Cornuet. 1999. Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J. Hered. 90:502-503.
41. Posada, D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
42. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
43. R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
44. Rambaut, A. (2009) FigTree version 1.3.1:Tree Figure Drawing Tool. Institute of Evolutionary Biology, University of Edinburgh, http://tree.bio.ed.ac.uk/.
45. Rambaut, A., and A. J. Drummond (2009) Tracer v1.4. http://evolve.zoo.ox.ac.uk/.
46. Raymond, M., and F. Rousset. 1995. GENEPOP (Version-1.2) - Population genetics software for exact tests and ecumenicism. J. Hered. 86:248-249.
47. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572.
48. Rozas, J., J. C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496.
49. Spurgin, L. G., J. C. Illera, T. H. Jorgensen, D. A. Dawson, and D. S. Richardson. 2014. Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation? Mol. Ecol. 23:1028-1039.
50. Suárez, N. M., E. Betancor, T. E. Klassert, T. Almeida, M. Hernández, and J. J. Pestano. 2009. Phylogeography and genetic structure of the Canarian common chaffinch (Fringilla coelebs) inferred with mtDNA and microsatellite loci. Mol. Phylogenet. Evol. 53:556-564.
51. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
52. Weir, J., and D. Schluter. 2008. Calibrating the avian molecular clock. Mol. Ecol. 17:2321-2328.
53. Whittaker, R. J. 1998. Island Biogeography. Ecology, Evolution, and Conservation. Oxford University Press, New York.
54. Williamson-Natesan, E. G. 2005. Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv. Genet. 6:551-562.
55. Worley, K., C. Strobeck, S. Arthur, J. Carey, H. Schwantje, A. Veitch, et al. 2004. Population genetic structure of North American thinhorn sheep (Ovis dalli). Mol. Ecol. 13:2545-2556.
56. Zhang, D. X., and G. M. Hewitt. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12:563-584.