Good human phylogeography

Over the past few years I have cast a skeptical eye at human phylogeography. Researchers like Spencer Wells have parlayed the study of uniparental lineages into books and television specials. Taking gene trees constructed from the Y chromosome Wells fashions the story of our species, in particular, of men. The problem of course is that Wells is looking at the lineage of the Y chromosome only! Humans are not neat little vacuum packages, nor are populations, rather, we are messy amalgamations of discrete genetic coalitions which are always in flux. Primed by our cultural mythologies and likely our mental biases we jump at neat and simple narratives, and in this day and age a scientific patina only makes it all the more sweeter. But we live in the post-genomic era, and as more and more data begins to push its way to the table I suspect that a readjustment of our plain yarns is inevitable. But not all of human phylogeography is worthless, one has to pick one's battles. Consider the recent work investigating the genetic impact of the Anglo-Saxon migrations. Or, consider this paper, Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders (full PDF). The authors found that a little more than 10% of the Balinese Y chromosomes seem to be Indian in origin. This is important, Bali is the last major refuge of Southeast Asian Hinduism. The historical mythologies of the pre-Islamic Hindu-Buddhist kingdoms of Austronesia imply that there was an emigration of notables from the kingdoms of southern India, particular from what is today Tamil Nadu, which reshaped the cultural landscape of the region. India and Bali are geographically distinct enough that the signal of exogenous lineages should be detectable, and it seems they are. Additionally, Bali is an island, which minimizes the possibilities for continuous genetic exchange with surrounding populations. Finally, we know the vague outlines of Bali's history, so that we can bring to bear other disciplines to fine tune our probabilities of plausibility. Whether South Asians influenced Bali genetically as well as culturally is not as grand a question as "where does our species come from?" But, it is modest enough and narrow enough that one can imagine a testable hypothesis. Unlike the origins of our species the history of Bali is somewhat illuminated by its own written records & mythologies, we are not flying in the dark relying on DNA only. The objective is tenable, and the tools are at our disposal are variegated and diverse.