The present work describes the basic principles underlying demographic reconstructions from genetic data, and reviews the studies using such methods with respect to the Neolithic Demographic Transition. It is intended as a tool for scholars outside the field of population genetics (e.g., archaeologists, anthropologists, etc.) to better understand the significance and intrinsic limitations of genetic demography, and to help integrate its results within the broader context of the reconstruction of the human past.
A new preprint to which I have contributed is now out on bioRxiv.
When temperate species living in the northern hemisphere are genetically differentiated for no apparent reason, it is likely due to what happened during the last Ice Age.
The expansion of the ice sheets around 21,000 years ago led many species to move to the so-called “glacial refugia”, areas further south where the climate remained milder. If there were multiple refugia isolated from each other, what was previously a single population could divide and differentiate, and then maintain this genetic structure when returning north after the end of the glaciation.
This has happened to many species. It is important, however, not to assume that it’s the reason behind the genetic structure of any species. We tested this hypothesis for the Yellow Warbler (Setophaga petechia), a small passerine bird living in North America.
Male Yellow Warbler (Setophaga petechia). Photo by Alan Vernon on Flickr. Distributed under the CC BY-NC-SA 2.0 license
A study on this species found a clear genetic structure: Eastern and Western populations west are quite different from each other, while those living in the middle have intermediate characteristics.
In our study, we explicitly simulated the genetic history of this little bird over the past 50,000 years. In this way, we were able to test whether during the glacial maximum (around 21,000 years ago) the species moved to single or multiple refugia, and what happened during the repopulation of North America after the end of the Ice Age.
By doing so, we were able to demonstrate that the yellow warbler had only one glacial refugium; the observed genetic diversity observed is the result of an asymmetric expansion. Ice sheets retreated at different times in the East and the West, and populations moved northward at different times, which created the genetic structure we see today.
It is important to remember that multiple glacial refugia are only one of the possible explanations for modern-day genetic structure: instead of assuming it we should test if it is the most likely explanation for any species of interest.
During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, insular populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. However, an alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American Yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. Using a climate-informed spatial genetic modelling (CISGeM) framework, we were able to reconstruct past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The contemporary population structure observed in the data was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure.
