Genetic landscapes showing human genetic diversity aligning with geography

New preprint at BioRxiv, Genetic landscapes reveal how human genetic diversity aligns with geography, by Peter, Petkova, and Novembre (2017).


Summarizing spatial patterns in human genetic diversity to understand population history has been a persistent goal for human geneticists. Here, we use a recently developed spatially explicit method to estimate “effective migration” surfaces to visualize how human genetic diversity is geographically structured (the EEMS method). The resulting surfaces are “rugged”, which indicates the relationship between genetic and geographic distance is heterogenous and distorted as a rule. Most prominently, topographic and marine features regularly align with increased genetic differentiation (e.g. the Sahara desert, Mediterranean Sea or Himalaya at large scales; the Adriatic, inter-island straits in near Oceania at smaller scales). We also see traces of historical migrations and boundaries of language families. These results provide visualizations of human genetic diversity that reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, there have regularly been factors that subtly distort the underlying relationship across space observed today. The fine-scale population structure depicted here is relevant to understanding complex processes of human population history and may provide insights for geographic patterning in rare variants and heritable disease risk.

Regional patterns of genetic diversity. a: scale bar for relative effective migration rate. Posterior effective migration surfaces for b: Western Eurasia (WEA) e: Central/Eastern Eurasia (CEA) g: Africa (AFR) h Southern African hunter-gatherers (SAHG) k: and Southeast Asian (SEA) analysis panels. ‘X’ marks locations of samples noted as displaced or recently admixed, ‘H’ denotes Hunter-Gatherer populations (both ‘X’ and ‘H’ samples are omitted from the EEMS model fit); in panel g, red circles indicate Nilo-Saharan speakers and in panel h, ‘B’ denotes Bantu-speaking populations. Approximate location of troughs are shown with dashed lines (see Extended Data Figure 4). PCA plots: c: WEA d:Europeans in WEA f: CEA i: SAHG j: AFR l: SEA. Individuals are displayed as grey dots. Large dots reflect median PC position for a sample; with colors reflecting geography matched to the corresponding EEMS figure. In the EEMS plots, approximate sample locations are annotated. For exact locations, see annotated Extended Data Figure 4 and Table S1. Features discussed in the main text and supplement are labeled. FST values per panelemphasize the low absolute levels of differentiation.”

Among ‘effective migration surfaces‘ (or potential past migration routes), the Pontic-Caspian steppe and its most direct connection with the Carpathian basin, the Danubian plains, appear maybe paradoxically as a constant ‘trough’ (below average migration rate) in all maps.

After all, we could have agreed that this region should be a priori thought as the route of many migrations from the steppe and Asia into Central Europe (and thus of ‘effective migration’) in prehistoric, proto-historic and historic times, such as Suvorovo-Novodanilovka (Pre-Anatolian), Yamna (Late Indo-European), probably Srubna, Scythian-Cimmerian, Sarmatian, Huns, Goths, Avars, Slavs, Mongols

It most likely (at least partially) represents a rather recent historical barrier to admixture, involving successive Byzantine, South Slavic, and Ottoman spheres of influence positioned against Balto-Slavic societies of Eastern Europe.

Location of troughs in West Eurasia (below average migration rate in more than 95% of MCMC iterations) are given in brown. Sample locations and EEMS grid are displayed for the West Eurasian analysis panel. FST values are provided per panel to emphasize the low absolute levels of differentiation.

Featured image, from the article: “Large-scale patterns of population structure. a: EEMS posterior mean effective migration surface for Afro-Eurasia (AEA) panel. ‘X’ marks locations of samples excluded as displaced or recently admixed. ‘H marks locations of excluded hunter-gatherer populations. Regions and features discussed in the main text are labeled. Approximate locations of troughs are annotated with dashed lines (see Extended Data Figure 4). b: PCA plot of AEA panel: Individuals are displayed as grey dots, colored dots reflect median of sample locations; with colors reflecting geography and matching with the EEMS plot. Locations displayed in the EEMS plot reflect the position of populations after alignment to grid vertices used in the model (see methods).”

Images and text available under a CC-BY-NC-ND 4.0 International License.

Discovered via Razib Khan’s blog.


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