• Alexandrino J, Arntzen JW, Ferrand N (2002) Nested clade analysis and the genetic evidence for or population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela). Heredity, 88, 6674.
  • Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
  • Hey JCA, Machado CA (2003) The study of structured populations — new hope for a difficult and divided science. Nature Reviews Genetics, 4, 535543.
  • Johnson JA, Dunn PO, Bouzat JL (2007) Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens. Molecular Ecology, 16, 22032222.
  • Knowles LL (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17, 110.
  • Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 26232635.
  • Masta SE, Laurent NM, Routman EJ (2003) Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analysis. Molecular Ecology, 12, 15411554.
  • Panchal M (2007) The automation of nested clade phylogeographic analysis. Bioinformatics, 23, 509510.
  • Panchal M, Beaumont MA (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution, 61, 14661480.
  • Paulo S, Jordan WC, Bruford MW, Nichols RA (2002) Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian lizard. Molecular Ecology, 11, 809819.
  • Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics, 161, 469471.
  • Posada D, Crandall KA, Templeton AR (2000) geodis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487488.
  • Smouse PE (1998) To tree or not to tree. Molecular Ecology, 7, 399412.
  • Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381397.
  • Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology, 10, 779791.
  • Templeton AR (2002) ‘Optimal’ randomization strategies when testing the existence of a phylogeographic structure: a reply to Petit and Grivet. Genetics, 161, 473475.
  • Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789809.
  • Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial-DNA haplotypes in the Tiger Salamander, Ambystoma tigrinum. Genetics, 140, 767782.
  • Wakeley J (2003) Inferences about the structure and history of populations: coalescents and intraspecific phylogeography. In: The Evolution of Population Biology (eds SinghR, UyenoyamaM), pp. 193215. Cambridge University Press, Cambridge, UK.
  • Weiss S, Ferrand N (2006) Current perspectives in phylogeography and the significance of South European refugia in the creation and maintenance of European biodiversity. In: Phylogeography of Southern European Refugia (eds WeissS, FerrandN), pp. 341357. Springer, Amsterdam, The Netherlands.
  • Zhang A-B, Tan S, Sota T (2006) autoinfer 1.0: a computer program to infer biogeographical events automatically. Molecular Ecology Notes, 6, 597599.