A Comparative View of Comparative Phylogeography

A recent issue of PNAS includes papers from a Sackler Colloquium on comparative phylogeography. As stated by the organizers, a major purpose of that gathering “was to bring together leading scientists to address the current state of phylogeography as the discipline enters its fourth decade” (Avise et al. 2016).

Four decades?!?

Time flies when the collective goal is identifying evolutionary processes that generated the spatial genetic patterns of (ideally) every species on Earth. Even comparative phylogeography, which synthesizes across single-species phylogeographies to understand how evolution and environment interact at the community scale, is a ripe old age of 30.

Comparative phylogeography occupies an intermediate position between landscape-level investigations and evolutionary biogeographic studies at higher taxonomic levels.

Comparative phylogeography occupies an intermediate position between landscape-level investigations and evolutionary biogeographic studies at higher taxonomic levels. (Figure 7 from Riddle (2016)).

As a contribution to that PNAS issue, Brett Riddle writes a timely review of the field of comparative phylogeography (“CP”). His review is focused specifically on continental systems, and it uses a database of 455 studies to assess trends and biases in the field to date. I talk about a few highlights below (hopefully inspiring you to read the paper in full).

Of course, dataset size and scope exhibit major trends in CP over the past 15 years. Not unexpectedly, Riddle finds that the size and genomic scope of phylogeographic datasets has increased across this period. However, it is also clear that few CP studies are using nuclear data to the exclusion of organelle genomes. This is because:

…organelle DNA, particularly mitochondrial DNA in animals, still likely delivers a very strong and heuristically valuable first approximation of geographic genetic architecture. (Riddle 2016)

Riddle (rightly) points out that organellar DNA is heuristically valuable as well; it can be used to generate hypotheses of past or present secondary contact and introgression. Those hypotheses can then be robustly tested with larger, potentially genomic-scale datasets.

Another trend is in the geographic focus of CP studies. We should celebrate the notable increases in the proportion of studies focused on the Southern Hemisphere. Riddle also recovers a near-global distribution of CP ‘hotspots’ – regions where studies are proliferating and might shed a particularly bright light on community-level evolution.

Yet, there are conspicuous directions in which CP could profitably expand – but hasn’t. For example, incorporation of biological or ecological relationships into CP studies is rare. That is an important direction to pursue because phylogeographic patterns of codistributed taxa are more richly compared and contrasted in light of basic natural history data. Another gap is the focus on trait evolution. If biological or ecological factors are indeed suspected to be driving evolution below the species level, then quantifying traits relevant to these factors may help to explain phylogeographic patterns. Finally, a few regions continue to be underrepresented in CP in general (Middle East, India, Tibetan Plateau).

Each of Riddle’s proposed ways forward for CP is sound; an overarching theme is that there is much to gain by interfacing with other disciplines. Yes, genomic-scale data will continue to help resolve fine-scale phylogeographic patterns and reveal cryptic instances of past contact. But equally auspicious for CP will be advances outside the field of molecular evolution: improved distribution modeling, more precise and higher-resolution trait data, new fossil discoveries, and continued refinement of existing geological and climatic hypotheses.


Avise, J. C., Bowen, B. W., and Ayala, F. J.. 2016. In the light of evolution X: Comparative phylogeography. Proceedings of the National Academy of Sciences 113: 7957-7961.

Riddle, B. R. 2016. Comparative phylogeography clarifies the complexity and problems of continental distribution that drove AR Wallace to favor islands. Proceedings of the National Academy of Sciences 113: 7970-7977.

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