Li WH, Gojobri T, Nei M: Pseudogenes as a paradigm of neutral evolution. Nature. 1981, 292: 237-239. 10.1038/292237a0.
Article
CAS
PubMed
Google Scholar
Nachman MW, Crowell SL: Contrasting evolutionary histories of two introns of the Duchenne muscular dystrophy gene, Dmd, in humans. Genetics. 2000, 155: 1855-1864.
PubMed Central
CAS
PubMed
Google Scholar
Leicht BG, Muse SV, Hanczyc M, Clarck AG: Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila . Genetics. 1995, 139: 299-308.
PubMed Central
CAS
PubMed
Google Scholar
Prager EM, Orrego C, Sage RD: Genetic variation and phylogeography of central Asian and other House Mice, including a major new mitochondrial lineage in Yemen. Genetics. 1998, 150: 835-861.
PubMed Central
CAS
PubMed
Google Scholar
Martinez-Arias R, Calafell F, Mateu E, Comas D, Andrés A, Bertranpetit J: Sequence variability of a human pseudogene. Genome Res. 2001, 11: 1071-1085. 10.1101/gr.GR-1677RR.
Article
PubMed Central
CAS
PubMed
Google Scholar
Avise JC: Molecular markers, natural history, and evolution. 1994, New York: Chapman and Hall
Book
Google Scholar
Ellegren H: Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet. 2000, 16: 551-558. 10.1016/S0168-9525(00)02139-9.
Article
CAS
PubMed
Google Scholar
Kimura M, Crow JF: The number of alleles that can be maintained in a finite population. Genetics. 1964, 49: 725-738.
PubMed Central
CAS
PubMed
Google Scholar
Ohta T, Kimura M: A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res. 1973, 22: 201-204.
Article
CAS
PubMed
Google Scholar
Begun DJ, Aquadro CF: Levels of naturally occurring DNA polymorphism correlate with recombination rates in Drosophila melanogaster. Nature. 1992, 356: 519-520. 10.1038/356519a0.
Article
CAS
PubMed
Google Scholar
Kreitman M, Akashi H: Molecular evidence for natural selection. Ann Rev Ecol Syst. 1995, 26: 403-422. 10.1146/annurev.es.26.110195.002155.
Article
Google Scholar
Hedrick PW: Perspective: Highly variable loci and their interpretation in evolution and conservation. Evolution. 1999, 53: 313-318.
Article
Google Scholar
Palumbi SR, Baker CS: Contrasting population structure from nuclear intron and mtDNA of humpback whales. Mol Biol Evol. 1994, 11: 426-435.
CAS
PubMed
Google Scholar
Friesen VL, Congdon BC, Walsh HE, Birt TP: Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms. Mol Ecol. 1997, 6: 1047-1058. 10.1046/j.1365-294X.1997.00277.x.
Article
CAS
PubMed
Google Scholar
Congdon BC, Piatt JF, Martin K, Freisen V: Mechanisms of population differentiation in marbled murrelets: Historical versus contemporary processes. Evolution. 2000, 54: 974-986.
Article
CAS
PubMed
Google Scholar
Karl SA, Avise JC: PCR-based assays of Mendelian polymorphisms from anonymous single-copy nuclear DNA: Techniques and applications for population genetics. Mol Biol Evol. 1993, 10: 342-361.
CAS
PubMed
Google Scholar
Holder K, Montgomerie R, Friesen VL: A test of the glacial refugium hypothesis using patterns of mitochondrial and nuclear DNA sequence variation in rock ptarmigam (Lagopus mutus). Evolution. 1999, 53: 1936-1950.
Article
CAS
Google Scholar
Vallianatos M, Lougheed SC, Boag PT: Conservation of the loggerhead shrike (Lanius ludovicianus) in central and eastern North America. Cons Genet. 2002, 3: 1-13. 10.1023/A:1014232326576.
Article
CAS
Google Scholar
Brumfield RT, Beerli P, Nickerson DA, Edwards SV: The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol. 2003, 18: 249-256. 10.1016/S0169-5347(03)00018-1.
Article
Google Scholar
Keith S, Urban EK, Fry CH: The birds of Africa. 1992, New York: Academic Press, 4:
Google Scholar
Smith TB, Wayne RK, Girman DJ, Bruford MW: A role for ecotones in generating rainforest biodiversity. Science. 1997, 276: 1855-1857. 10.1126/science.276.5320.1855.
Article
CAS
Google Scholar
Smith TB, Calsbeek R, Wayne RK, Pires DB, Bardeleben C: Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird. J Evol Biol. 2005, 18: 257-268. 10.1111/j.1420-9101.2004.00825.x.
Article
CAS
PubMed
Google Scholar
Maley J: The impact of arid phases on the African rainforest through geologic history. African rain forest ecology and conservation. Edited by: Weber W, White LJT, Vedder A. 2001, New Haven: Yale University Press, 68-87.
Google Scholar
Smith TB, Schneider CJ, Holder K: Refugual isolation versus ecological gradients. Genetica. 2001, 112–113: 383-398. 10.1023/A:1013312510860.
Article
PubMed
Google Scholar
Hess CM, Gasper J, Hoekstra HE, Hill CE, Edwards SV: Mhc class II pseudogene and genomic signature of a 32-kb cosmid in the house finch (Carpodacus mexicanus). Genome Res. 2000, 10: 613-623. 10.1101/gr.10.5.613.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grimsley C, Mather KA, Ober C: HLA-H: Pseudogene with increased variation due to balancing selection at neighboring loci. Mol Biol Evol. 1998, 15: 1581-1588.
Article
CAS
PubMed
Google Scholar
Slatkin M, Hudson RR: Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991, 129: 555-562.
PubMed Central
CAS
PubMed
Google Scholar
Rogers AR, Harpending H: Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992, 9: 552-569.
CAS
PubMed
Google Scholar
Pogson GH: Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). Genetics. 2001, 157: 317-330.
PubMed Central
CAS
PubMed
Google Scholar
Saez AG, Tatarenkov A, Barrio E, Becerra NH, Ayala FJ: Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep. Proc Natl Acad Sci (USA). 2003, 100: 1793-1798. 10.1073/pnas.242746799.
Article
CAS
Google Scholar
Ptak SE, Przeworski M: Evidence for population growth in humans is confounded by fine-scale population structure. Trend Genetics. 2002, 18: 559-563. 10.1016/S0168-9525(02)02781-6.
Article
Google Scholar
Hammer MF, Blackmer F, Garrigan D, Nachman MW, Wilder JA: Human population structure and its effects on sampling Y chromosome sequence variation. Genetics. 2003, 164: 1495-1509.
PubMed Central
CAS
PubMed
Google Scholar
Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: a laboratory manual. 1989, New York: Cold Spring Harbor Laboratory Press
Google Scholar
Sunnucks P, Wilson ACC, Beheregary LB, Zenger K, French J, Taylor AC: SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol Ecol. 2000, 9: 1699-1710. 10.1046/j.1365-294x.2000.01084.x.
Article
CAS
PubMed
Google Scholar
Edwards SV, Gasper J, March M: Genomics and polymorphism of Agph-DAB1, an Mhc class II gene in Red-winged Blackbirds (Agelaius phoecineus). Mol Biol Evol. 1998, 15: 236-250.
Article
CAS
PubMed
Google Scholar
Belkhir K: GENETIX (v4.04): A Windows program for population genetic analysis. 1999, Laboratorie Genome, Populations: Interactions UPR 5000 du CNRS, Universite Montpellier II, Montpellier (France)
Google Scholar
Raymond M, Rousset F: GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. J Heredity. 1995, 86: 248-249.
Google Scholar
Tajima F: Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989, 123: 585-595.
PubMed Central
CAS
PubMed
Google Scholar
Fu YX, Li WH: Statistical tests of neutrality of mutations. Genetics. 1993, 133: 693-709.
PubMed Central
CAS
PubMed
Google Scholar
Rosas J, Rosas R: DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics. 1999, 15: 174-175. 10.1093/bioinformatics/15.2.174.
Article
Google Scholar
Weir BS, Cockerham CC: Estimating F statistics for the analysis of population structure. Evolution. 1984, 38: 1358-1370.
Article
Google Scholar
Hudson RR, Slatkin M, Maddison WP: Estimation of levels of gene flow from DNA sequence data. Genetics. 1992, 132: 582-589.
Google Scholar
Kalinowski ST: HP-RARE: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol. 2005, 5: 187-189. 10.1111/j.1471-8286.2004.00845.x.
Article
CAS
Google Scholar
Machado CA, Kliman RM, Markert JA, Hey J: Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Mol Biol Evol. 2002, 19: 472-288.
Article
CAS
PubMed
Google Scholar
Hey J, Wakeley J: A coalescent estimator of the population recombination rate. Genetics. 1997, 145: 833-846.
PubMed Central
CAS
PubMed
Google Scholar
Nei M: Molecular Evolutionary Genetics. 1987, New York: Columbia University Press
Google Scholar
POPULATIONS (v 1.2.28). [http://www.cnrs-gif.fr/pge/bioinfo/populations/]