Gene Trees and Organismal Histories: a Phylogenetic Approach to Population Biology.

A "gene tree" is the phylogeny of alleles or haplotypes for any specified stretch of DNA. Gene trees are components of population trees or species trees; their analysis entails a shift in perspective from many of the familiar models and concepts of population genetics, which typically deal with frequencies of phylogenetically unordered alleles. Molecular surveys of haplotype diversity in mitochondrial DNA (mtDNA) have provided the first extensive empirical data suitable for estimation of gene trees on a microevolutionary (intraspecific) scale. The relationship between phylogeny and geographic distribution constitutes the phylogeographic pattern for any species. Observed phylogeographic trees can be interpreted in terms of historical demography by comparison to predictions derived from models of gene lineage sorting, such as inbreeding theory and branching-process theory. Results of such analyses for more than 20 vertebrate species strongly suggest that the demographies of populations have been remarkably dynamic and unsettled over space and recent evolutionary time. This conclusion is consistent with ecological observations documenting dramatic population-size fluctuations and range shifts in many contemporary species. By adding an historical perspective to population biology, the gene-lineage approach can help forge links between the disciplines of phylogenetic systematics (and macroevolutionary study) and population genetics (microevolution). Preliminary extensions of the "gene tree" methodology to haplotypes of nuclear genes (such as Adh in Drosophila melanogaster) demonstrate that the phylogenetic perspective can also help to illuminate molecular-genetic processes (such as recombination or gene conversion), as well as contribute to knowledge of the origin, age, and molecular basis of particular adaptations.