phylogeography
Brito PH & Edwards SV 2009 Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439-455.
- the phylogenetic tradition
- the discordance found was often ascribed not to independent realizations of the lineage sorting process
- but rather to sampling error at the level of nucleotides ad nucleotide substitution models
- the tacit assumption is that all genes do in fact have the same gene tree
- that these gene trees are congruent with and converge on the species tree
- that concatenation will iron-out any inconsistencies in phylogenetic signal among genes
- the concept of "statistical phylogeography" (Knowles and Maddison 2002) formalized the study of geographic patterns of genetic variation via gene trees
- by stressing the importance of defining phylogeographic hypotheses to be contrasted at the population level, rather than at the level of gene trees
