Susanne P. Pfeifer

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

Going Ape Over Genetic Maps Recombination is an important process in generating diversity and producing selectively advantageous genetic combinations. Thus, changes in recombination hotspots may influence speciation. To investigate the variation in recombination processes in humans and their closest existing relatives, Auton et al. (p. 193, published online 15 March) prepared a fine-scale genetic map of the Western chimpanzee and compared it with that of humans. While rates of recombination are comparable between humans and chimpanzees, the locations and genetic motifs associated with recombination differ between the species. Chimpanzees show similar genetic recombination rates as humans but differ in the genomic regions involved. To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

Balancing Humans with Apes Shared ancestral polymorphisms between species tend to be relatively rare, and studies of trans-species polymorphisms have focused on just a few regions known for balancing selection. Leffler et al. (p. 1578, published online 14 February) performed genome-wide scans among humans and great apes and found shared polymorphisms between chimps and humans. Many of the identified variants seem to be associated with genes involved in pathogen response or defense, suggesting that this widespread balancing selection may reflect the ongoing arms race between pathogens and hosts. Genome-wide shared genetic polymorphisms between humans and chimps mostly affect host-pathogen interactions. Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.

Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germline.

Significance Harvey rat sarcoma viral oncogene homolog (HRAS) occupies an important place in medical history, because it was the first gene in which acquired mutations that led to activation of a normal protein were associated with cancer, making it the prototype of the now canonical oncogene mechanism. Here, we explore what happens when similar HRAS mutations occur in male germ cells, an issue of practical importance because the mutations cause a serious congenital disorder, Costello syndrome, if transmitted to offspring. We provide evidence that the mutant germ cells are positively selected, leading to an increased burden of the mutations as men age. Although there are many parallels between this germline process and classical oncogenesis, there are interesting differences of detail, which are explored in this paper. The RAS proto-oncogene Harvey rat sarcoma viral oncogene homolog (HRAS) encodes a small GTPase that transduces signals from cell surface receptors to intracellular effectors to control cellular behavior. Although somatic HRAS mutations have been described in many cancers, germline mutations cause Costello syndrome (CS), a congenital disorder associated with predisposition to malignancy. Based on the epidemiology of CS and the occurrence of HRAS mutations in spermatocytic seminoma, we proposed that activating HRAS mutations become enriched in sperm through a process akin to tumorigenesis, termed selfish spermatogonial selection. To test this hypothesis, we quantified the levels, in blood and sperm samples, of HRAS mutations at the p.G12 codon and compared the results to changes at the p.A11 codon, at which activating mutations do not occur. The data strongly support the role of selection in determining HRAS mutation levels in sperm, and hence the occurrence of CS, but we also found differences from the mutation pattern in tumorigenesis. First, the relative prevalence of mutations in sperm correlates weakly with their in vitro activating properties and occurrence in cancers. Second, specific tandem base substitutions (predominantly GC>TT/AA) occur in sperm but not in cancers; genomewide analysis showed that this same mutation is also overrepresented in constitutional pathogenic and polymorphic variants, suggesting a heightened vulnerability to these mutations in the germline. We developed a statistical model to show how both intrinsic mutation rate and selfish selection contribute to the mutational burden borne by the paternal germline.

Loci associated with skin pigmentation identified in African populations

African genomics and skin color Skin color varies among human populations and is thought to be under selection, with light skin maximizing vitamin D production at higher latitudes and dark skin providing UV protection in equatorial zones. To identify the genes that give rise to the palette of human skin tones, Crawford et al. applied genome-wide analyses across diverse African populations (see the Perspective by Tang and Barsh). Genetic variants were identified with likely function in skin phenotypes. Comparison to model organisms verified a conserved function of MFSD12 in pigmentation. A global genetic panel was used to trace how alleles associated with skin color likely moved across the globe as humans migrated, both within and out of Africa. Science, this issue p. eaan8433; see also p. 867 Genome-wide analysis of 2000 Africans identifies and functionally characterizes pigmentation loci. INTRODUCTION Variation in pigmentation among human populations may reflect local adaptation to regional light environments, because dark skin is more photoprotective, whereas pale skin aids the production of vitamin D. Although genes associated with skin pigmentation have been identified in European populations, little is known about the genetic basis of skin pigmentation in Africans. RATIONALE Genetically and phenotypically diverse African populations are informative for mapping genetic variants associated with skin pigmentation. Analysis of the genetics of skin pigmentation in Africans informs upon melanocyte biology and the evolution of skin pigmentation in humans. RESULTS We observe extensive variation in skin pigmentation in Africa, with lowest melanin levels observed in southern African San hunter-gatherers and highest levels in East African Nilo-Saharan pastoralists. A genome-wide association study (GWAS) of 1570 Africans identified variants significantly associated with skin pigmentation, which clustered in four genomic regions that together account for almost 30% of the phenotypic variation. The most significantly associated single-nucleotide polymorphisms were at SLC24A5, a gene associated with pigmentation in Europeans. We show that SLC24A5 was introduced into East Africa >5 thousand years ago (ka) and has risen to high frequency. The second most significantly associated region is near the gene MFSD12. Using in vitro and in vivo analyses, we show that MFSD12 codes for a lysosomal protein that modifies pigmentation in human melanocytes, with decreased MFSD12 expression associated with darker pigmentation. We also show that genetic knockout of Mfsd12 affects pigmentation in mice. A third highly associated region encompasses a cluster of genes that play a role in ultraviolet (UV) response and DNA damage repair. We find the strongest associations in a regulatory region upstream of DDB1, the gene encoding damage-specific DNA binding protein 1, and that these variants are associated with increased expression of DDB1. The alleles associated with light pigmentation swept to near fixation outside of Africa due to positive selection, and we show that these lineages coalesce ~60 ka, corresponding with the time of migration of modern humans out of Africa. The fourth significantly associated region encompasses the OCA2 and HERC2 loci. We identify previously uncharacterized variants at HERC2 associated with the expression of OCA2. These variants arose independently from eye and skin pigmentation–associated variants in non-Africans. We also identify variants at OCA2 that are correlated with alternative splicing; alleles associated with light pigmentation are correlated with a shorter transcript, which lacks a transmembrane domain. CONCLUSION We identify previously uncharacterized genes and variants associated with skin pigmentation in ethnically diverse Africans. These genes have diverse functions, from repairing UV damage to playing important roles in melanocyte biology. We show that both dark and light pigmentation alleles arose before the origin of modern humans and that both light and dark pigmented skin has continued to evolve throughout hominid history. We show that variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. This study sheds light on the evolutionary history, and adaptive significance, of skin pigmentation in humans. GWAS and functional assays illuminate the genetic basis of pigmentation in Africa. A GWAS identified four genomic regions associated with skin pigmentation in Africa. Functional assays in melanocytes and mice characterized their impact on skin pigmentation. Evolutionary genetic analyses revealed that most derived variants evolved before the origin of modern humans. Ma, million years ago. Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.

Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus cowlesi and Aspidoscelis inornata, for which previous research has linked mutations in the melanocortin‐1 receptor gene (Mc1r) to blanched coloration. We sampled populations both on and off the dunes and used a custom sequence capture assay based on probed fosmid libraries to obtain >50 kb of sequence around Mc1r and hundreds of other random genomic locations. We then used model‐based statistical inference methods to describe the demographic and adaptive history characterizing the colonization of White Sands. We identified a number of similarities between the two focal species, including strong evidence of selection in the blanched populations in the Mc1r region. We also found important differences between the species, suggesting different colonization times, different genetic architecture underlying the blanched phenotype and different ages of the beneficial alleles. Finally, the beneficial allele is dominant in S. cowlesi and recessive in A. inornata, allowing for a rare empirical test of theoretically expected patterns of selective sweeps under these differing models.

From next-generation resequencing reads to a high-quality variant data set

Sequencing has revolutionized biology by permitting the analysis of genomic variation at an unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it accessible for a wide range of research topics. However, the produced data contain subtle but complex types of errors, biases and uncertainties that impose several statistical and computational challenges to the reliable detection of variants. To tap the full potential of high-throughput sequencing, a thorough understanding of the data produced as well as the available methodologies is required. Here, I review several commonly used methods for generating and processing next-generation resequencing data, discuss the influence of errors and biases together with their resulting implications for downstream analyses and provide general guidelines and recommendations for producing high-quality single-nucleotide polymorphism data sets from raw reads by highlighting several sophisticated reference-based methods representing the current state of the art.

Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective

Given the strong selective pressures often faced by populations when colonizing a novel habitat, the level of variation present on which selection may act is an important indicator of adaptive potential. While often discussed in an ecological context, this notion is also highly relevant in our clinical understanding of viral infection, in which the novel habitat is a new host. Thus, quantifying the factors determining levels of variation is of considerable importance for the design of improved treatment strategies. Here, we focus on such a quantification of human cytomegalovirus (HCMV) – a virus which can be transmitted across the placenta, resulting in foetal infection that can potentially cause severe disease in multiple organs. Recent studies using genomewide sequencing data have demonstrated that viral populations in some congenitally infected infants diverge rapidly over time and between tissue compartments within individuals, while in other infants, the populations remain highly stable. Here, we investigate the underlying causes of these extreme differences in observed intrahost levels of variation by estimating the underlying demographic histories of infection. Importantly, reinfection (i.e. population admixture) appears to be an important, and previously unappreciated, player. We highlight illustrative examples likely to represent a single‐population transmission from a mother during pregnancy and multiple‐population transmissions during pregnancy and after birth.

The Demographic and Adaptive History of the African Green Monkey

Relatively little is known about the evolutionary history of the African green monkey (genus Chlorocebus) due to the lack of sampled polymorphism data from wild populations. Yet, this characterization of genetic diversity is not only critical for a better understanding of their own history, but also for human biomedical research given that they are one of the most widely used primate models. Here, I analyze the demographic and selective history of the African green monkey, utilizing one of the most comprehensive catalogs of wild genetic diversity to date, consisting of 1,795,643 autosomal single nucleotide polymorphisms in 25 individuals, representing all five major populations: C. a. aethiops, C. a. cynosurus, C. a. pygerythrus, C. a. sabaeus, and C. a tantalus. Assuming a mutation rate of 5.9 × 10-9 per base pair per generation and a generation time of 8.5 years, divergence time estimates range from 523 to 621 kya for the basal split of C. a. aethiops from the other four populations. Importantly, the resulting tree characterizing the relationship and split-times between these populations differs significantly from that presented in the original genome paper, owing to their neglect of within-population variation when calculating between population-divergence. In addition, I find that the demographic history of all five populations is well explained by a model of population fragmentation and isolation, rather than novel colonization events. Finally, utilizing these demographic models as a null, I investigate the selective history of the populations, identifying candidate regions potentially related to adaptation in response to pathogen exposure.

Inferring the age of a fixed beneficial allele

Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype‐based estimators exist for inferring the age of segregating beneficial mutations. Here, we develop an approximate Bayesian‐based approach that rather estimates these parameters for fixed beneficial mutations in single populations. We integrate a range of existing diversity, site frequency spectrum, haplotype‐ and linkage disequilibrium‐based summary statistics. We show that for strong selective sweeps on de novo mutations the method can estimate allele age and selection strength even in nonequilibrium demographic scenarios. We extend our approach to models of selection on standing variation, and co‐infer the frequency at which selection began to act upon the mutation. Finally, we apply our method to estimate the age and selection strength of a previously identified mutation underpinning cryptic colour adaptation in a wild deer mouse population, and compare our findings with previously published estimates as well as with geological data pertaining to the presumed shift in selective pressure.

On the analysis of intrahost and interhost viral populations: Human cytomegalovirus as a case study of pitfalls and expectations

ABSTRACT Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovirus, the nucleotide diversity estimates are 10-fold higher for interhost data, while the number of segregating (i.e., polymorphic) sites is 6-fold lower. These results have been interpreted as demonstrating that sampled intrahost variants are strongly deleterious. In reality, however, these observations are fully consistent with standard population genetic expectations. Here, we analyze published intra- and interhost data sets within this framework, utilizing statistical inference tools to quantify the fitness effects of segregating mutations. Further, we utilize population level simulations to clarify expectations under common evolutionary models. Contrary to common claims in the literature, these results suggest that most observed polymorphisms are likely nearly neutral with regard to fitness and that standard population genetic models in fact well predict observed levels of both intra- and interhost variability. IMPORTANCE With the increasing number of evolutionary virology studies examining both intrahost and interhost patterns of genomic variation, a number of seemingly incompatible results have emerged, revolving around the far greater level of observed intrahost than interhost variation. This has led many authors to suggest that the great majority of sampled within-host polymorphisms are strongly deleterious. Here, we demonstrate that there is in fact no incompatibility of these results and, indeed, that the vast majority of sampled within-host variation is likely neutral. These results thus represent a major shift in the current view of observed viral variation.