Demographic models used for the coalescent simulations: A—population split at T₂ with two derived populations of the same size; B—population split at T₂ with two derived populations with ratio between their effective population sizes (N_EF) equal to 0.15; C—population split at T₂ with two derived populations with the ratio between their N_EFs equal to 0.06 at T₂ and 0.15 presently (T₀); D—same as model B, but with population substructure arising at T₁ in both derived populations; E—same as model C, but with population substructure arising at T₁ in both derived populations.

<p>The number of demes depicted does not correspond to the actual simulations. For further details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115449#sec002" target="_blank">methods</a> section.</p

Frequencies of the rs1815739 derived allele in autochthonous populations pooled into seven geographical groups.

<p>Frequencies of the rs1815739 derived allele in autochthonous populations pooled into seven geographical groups.</p

Differing Evolutionary Histories of the <i>ACTN3*R577X</i> Polymorphism among the Major Human Geographic Groups

<div><p>It has been proposed that the functional <i>ACTN3*R577X</i> polymorphism might have evolved due to selection in Eurasian human populations. To test this possibility we surveyed all available population-based data for this polymorphism and performed a comprehensive evolutionary analysis of its genetic diversity, in order to assess the action of adaptive and random mechanisms on its variation across human geographical distribution. The derived <i>577X</i> allele increases in frequency with distance from Africa, reaching the highest frequencies on the American continent. Positive selection, detected by an extended haplotype homozygosisty test, was consistent only with the Eurasian data, but simulations with neutral models could not fully explain the results found in the American continent. It is possible that particularities of Native American population structure could be responsible for the observed allele frequencies, which would have resulted from a complex interaction between selective and random factors.</p></div

Box plots of (A) Native American ancestry and (B) BMI for socioeconomic status bands 1 to 6 in the Antioquian study sample.

<p>Box plots of (A) Native American ancestry and (B) BMI for socioeconomic status bands 1 to 6 in the Antioquian study sample.</p

Distribution of (A) Native American ancestry and (B) socioeconomic status (bands 1 to 6) in Antioquian T2D cases and controls.

<p>Distribution of (A) Native American ancestry and (B) socioeconomic status (bands 1 to 6) in Antioquian T2D cases and controls.</p

Distribution of LOD-scores for disease association along the genome in the Antioquian T2D admixture mapping scan.

<p>Distribution of LOD-scores for disease association along the genome in the Antioquian T2D admixture mapping scan.</p

Sexual dimporphism on fWHR across socio-cultural categories.

<p>Box and whisker plots of a) fWHR sexual dimorphism in samples belonging to three different socio-cultural categories: HG: hunter-gatherers; F: farmers; SS: state societies. b) fWHR values of males from the Mexican general population (GP), males prosecuted by homicide (H), robbery (R) and other minor faults (O). Square: mean; box: standard error; whisker: standard deviation. c) Regression of fWHR on fitness, estimated as lifetime reproductive success (LRS, number of children raised to adulthood).</p

Databases used in this study. Population lists for each database are provided in Table S1.

1<p>: computed across all indices and across all populations.</p>2<p>: computed across all populations.</p>3<p>: computed across all indices. Indices definitions are as follows: WHR: Width-to heigth ratio, bizygomatic breadth/nasion-prosthion height; CI: Cephalic index, maximum cranial breadth ×100/maximum cranial length; CHLI: Cranial height-length, height (from bregma to basion or porion) ×100/maximum cranial length; CBHI: Cranial breadth-height, maximum cranial height ×100/maximum cranial breadth; CTI: Craniofacial transverse index, bizygomatic breadth ×100/maximum cranial breadth; GI: Gnathic index, basion-prosthion length ×100/basion-nasion length; JFI: Jugofrontal index, minimum frontal breadth ×100/bizygomatic breadth; OI: Orbital index: maximum orbital height ×100/maximum orbital breadth; NI: Nasal index: maximum nasal breadth ×100/nasal height; GP: Glabellar projection index, glabella-opisthocranion length/nasionopisthocranion length; NVI: Neurocranial volumetric index; FVI: Facial volumetric index; NFI: Neurofacial index; ANVI: Anteroneural volumetric index; MNVI: Midneural volumetric index; PNVI: Posteroneural volumetric index; OTVI: Otic volumetric index; OVI: Optic volumetric index; RVI: Respiratory volumetric index; MVI: Masticatory volumetric index; AVI: Alveolar volumetric index; ANMI: Anteroneural morphometric index; MNMI: Midneural morphometric index; PNMI: Posteroneural morphometric index; OTMI: Otic morphometric index; OMI: Optic morphometric index; RMI: Respiratory morphometric index; MMI: Masticatory morphometric index; AMI: Alveolar morphometric.</p

Genotypes, allele frequencies, and geographic locations of the Native American populations investigated.

1<p>Samples genotyped in present study  = 229;</p>2<p>Caution is needed regarding the classification of these modes of subsistence, since they are not stable over time and may not be unique. However, the two categories adopted here (agriculturalist and hunter-gatherer/forager) represent general pre-Columbian subsistence conditions of the investigated populations in accordance with what is known about them. AMOVA results: (a) Among the subdivisions (<i>F_CT</i>): 3.6% (<i>p</i> = 0.000); (b) Among populations within the Mesoamerican Agriculturalist subdivision (<i>F_ST):</i> 1.8% (<i>p</i> = 0.008); (c) Among populations within the South American hunter-gatherer/forager subdivision: 5.3% (<i>p</i> = 0.005); Among populations within the Andean Agriculturarist group: 0% (<i>p</i> = 0.36).</p

Sexual dimporphism on fWHR and further cranial indices.

<p>Box and whisker plots of global sexual dimorphism computed across the different databases. Indices that differed significantly among sexes (after t-test for independent samples) are shown in solid grey. A) Howells database; b) Pucciarelli database, c) 2D Geometric Morphometric database, d) 3D Geometric Morphometric database, e) Patagonian groups database. Square: median; box: 25%–75%; whisker: minimum-maximum values.</p