Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses

© 2018 Kanitz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Although it is generally accepted that geography is a major factor shaping human genetic differentiation, it is still disputed how much of this differentiation is a result of a simple process of isolation-by-distance, and if there are factors generating distinct clusters of genetic similarity. We address this question using a geographically explicit simulation framework coupled with an Approximate Bayesian Computation approach. Based on six simple summary statistics only, we estimated the most probable demographic parameters that shaped modern human evolution under an isolation by distance scenario, and found these were the following: an initial population in East Africa spread and grew from 4000 individuals to 5.7 million in about 132 000 years. Subsequent simulations with these estimates followed by cluster analyses produced results nearly identical to those obtained in real data. Thus, a simple diffusion model from East Africa explains a large portion of the genetic diversity patterns observed in modern humans. We argue that a model of isolation by distance along the continental landmasses might be the relevant null model to use when investigating selective effects in humans and probably many other species

Comparison between the STRUCTURE results obtained for observed (OBS) and simulated (SIM) data.

<p>Horizontal bars represent the 70 populations as used in the simulations and the different shades of gray code for the proportion of each inferred ancestry group (K from 2 to 4).</p

Distribution of estimated statistics from three simulated dataset and empirical observation (horizontal gray line).

<p>Within each plot, we present the different sources for the simulations that generated the distributions: “Prior” are simulations sampled randomly from the whole prior; “95%HPD” are simulations run based on the 95% higher posterior density estimates for all parameters; and “Mode” represent simulations based on the point estimates for all parameters.</p

Summary statistics in the adult barn owl population for all six microsatellite loci.

<p>Bp is for base pairs, NS for not significant after Bonferroni correction, ND for not tested, H-W for Hardy-Weinberg equilibrium, and HO and HE for observed and expected heterozygosity respectively.</p

Owl melanin-based plumage redness is more frequent near than away from the equator: implications on the effect of climate change on biodiversity

Climate change acts as a major new selective agent on many organisms, particularly at high latitudes where climate change is more pronounced than at lower latitudes. Studies are required to predict which species are at a high risk of extinction and whether certain phenotypes may be more affected by climate change than others. The identification of susceptible phenotypes is important for evaluating the potential negative effect of climate change on biodiversity at the inter- and intraspecific levels. Melanin-based coloration is an interesting and easily accessible candidate trait because, within certain species, reddish pheomelanin-based coloration is associated with adaptations to warm climates. However, it is unclear whether the same holds among species. We tested one prediction of this hypothesis in four owl genera (wood, scops, screech, and pygmy owls), namely that darker reddish species are more prevalent near the equator than polewards. Our comparative analysis is consistent with this prediction for the northern hemisphere, suggesting that pale reddish species may be adapted to cold climates and dark reddish species to warmer climates. Thus, climate change may have a larger negative impact on pale pheomelanic owls and favour dark pheomelanic species

PCA results in real observation and simulations.

<p>A, Comparison of PCA applied to the empirical data (left) and one selected simulation (right). The first (PC 1) and second (PC 2) principal components are represented here, where each point represents one of the analyzed populations, grouped by continents. B, Boxplots of the correlation values between the first two principal components in observations and simulations based on the prior distribution (“Prior”), 95% higher posterior density distribution (“95%HPD”), and on the point estimates (“Mode”).</p

Comparison of the patterns of isolation by distance generated with the empirical and simulated data.

<p>In A, the patterns obtained for the observed data; in B, the result of one of the simulations based on the point estimates. Each point represents a population (top) or a pairwise population comparison (bottom); the dashed lines represent the linear regressions of these points (whose R² values are informed).</p

Accuracy table and estimates of the six variable parameters inferred by the ABC framework.

<p>Point estimate corresponds to the mode of the posterior distribution, while HPD95% interval represents the parameter values comprised within the 95% higher posterior density interval. R² stands for the coefficient of determination of pseudo-observed on estimated values; SRMSE is the root mean squared error of the mode, standardized between 0 and 1; Prop. HPD95% stands for the proportion of tests for which 95% higher posterior density intervals include the true value. All rates are per generation (25 years).</p

Data from: The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved non-synonymous derived variant of the melanocortin-1-receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation

BarnOwlABC_Antoniazza_2014

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