Paradigm shifts in the phylogeographic analysis of seaweeds

Abstract

The phylogeographic analysis of seaweeds faces numerous biological, methodological, and conceptual challenges. One challenge is to understand how life-history phases, mating systems, dispersal mechanisms, and physiological tolerances influence the distributions and persistence of local populations. A second challenge has been to develop genetic assay methods that allow us to trace unbroken gene lineages so they can be tested with models using coalescence theory. An integral part of this challenge has been to identify unrecombining sections of DNA with known modes of inheritance. For the most part, seaweed phylogeographic studies have used unrecombining organellar and plastid DNAs, but new methods of phasing haplotypes of nuclear DNA can provide an enormous amount of data to fine-tune hypotheses to distinguish the effects of demography and natural selection. Finally, phylogeography faces conceptual challenges, as we learn ever more about palaeoclimates, the historical shapes of shorelines, and the dynamics of ocean currents. A major advance is the marriage between demographic models and models of natural selection, because both interact to mold the shapes of gene genealogies.