Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.

Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

Technical note: tree truthing: how accurate are substrate estimates in primate field studies?

Field studies of primate positional behavior typically rely on ground-level estimates of substrate size, angle, and canopy location. These estimates potentially influence the identification of positional modes by the observer recording behaviors. In this study we aim to test ground-level estimates against direct measurements of support angles, diameters, and canopy heights in trees at La Suerte Biological Research Station in Costa Rica. After reviewing methods that have been used by past researchers, we provide data collected within trees that are compared to estimates obtained from the ground. We climbed five trees and measured 20 supports. Four observers collected measurements of each support from different locations on the ground. Diameter estimates varied from the direct tree measures by 0-28 cm (Mean: 5.44 ± 4.55). Substrate angles varied by 1-55° (Mean: 14.76 ± 14.02). Height in the tree was best estimated using a clinometer as estimates with a two-meter reference placed by the tree varied by 3-11 meters (Mean: 5.31 ± 2.44). We determined that the best support size estimates were those generated relative to the size of the focal animal and divided into broader categories. Support angles were best estimated in 5° increments and then checked using a Haglöf clinometer in combination with a laser pointer. We conclude that three major factors should be addressed when estimating support features: observer error (e.g., experience and distance from the target), support deformity, and how support size and angle influence the positional mode selected by a primate individual. individual.

REJECTOR: software for population history inference from genetic data via a rejection algorithm.

UNLABELLED: We introduce REJECTOR, software for parameter estimation and comparison of alternate models of population history from genetic data via a rejection algorithm. Through coalescent simulation, REJECTOR generates numerous gene genealogies, and hence simulated data, under a model of population history specified by the user. Summary statistics derived from such simulated data are compared with observed statistics, leading to acceptance or rejection of a given set of parameter values. We performed tests of the software using known parameter values in order to assess the inferential power provided by each summary statistic. The tests demonstrate the precision and accuracy of estimation made possible using this approach. AVAILABILITY: http://www.rejector.org

IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing.

We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony to impute data marked as missing due to low coverage. Along with efficiently imputing missing variant genotypes, IMPUTOR is capable of reliably and accurately correcting many nonmissing sites that represent spurious sequencing errors. Tests on simulated data show that IMPUTOR is capable of detecting many induced mutations without making erroneous imputations/corrections, with as many as 95% of missing sites imputed and 81% of errors corrected under optimal conditions. We tested IMPUTOR with human Y-chromosomes from pairs of close relatives and demonstrate IMPUTOR's efficacy in imputing missing and correcting erroneous calls.

The shaping of modern human immune systems by multiregional admixture with archaic humans.

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.

SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes.

Each independently evolving segment of the genomes of a sexually reproducing organism has a separate history reflecting part of the evolutionary history of that organism. Uniparentally or clonally inherited DNA segments such as the mitochondrial and chloroplast genomes and the nonrecombining portion of the Y chromosome have provided, to date, most of the known data regarding compound haplotypic variation within and among populations. These comparatively small segments include numerous polymorphic sites and undergo little or no recombination. Recombining autosomes, however, comprise the major repository of genetic variation. Technical challenges and recombination have limited large-scale application of autosomal haplotypes. We have overcome this barrier through development of a general approach to the assessment of short autosomal DNA segments. Each such segment includes one or more single nucleotide polymorphisms (SNPs) and exactly one short tandem repeat (STR) locus. With dramatically different mutation rates, these two types of genetic markers provide complementary evolutionary information. We call the combination of a SNP and a STR polymorphism a SNPSTR, and have developed a simple, rapid method for empirically determining gametic phase for double and triple heterozygotes. Here, we illustrate the approach with two SNPSTR systems. Although even one system provides insight into population history, the power of the approach lies in combining results from multiple SNPSTR systems.