Recommendations for improving statistical inference in population genomics.

The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.

Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana.

It has recently been proposed that lower mutation rates in gene bodies compared with upstream and downstream sequences in Arabidopsis thaliana are the result of an "adaptive" modification of the rate of beneficial and deleterious mutations in these functional regions. This claim was based both on analyses of mutation accumulation lines and on population genomics data. Here, we show that several questionable assumptions were used in the population genomics analyses. In particular, we demonstrate that the difference between gene bodies and less selectively constrained sequences in the magnitude of Tajima's D can in principle be explained by the presence of sites subject to purifying selection and does not require lower mutation rates in regions experiencing selective constraints.

How chromosomal inversions reorient the evolutionary process.

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.

The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.

Current procedures for inferring population history generally assume complete neutrality-that is, they neglect both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the distribution of fitness effect as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites can be used to infer demographic histories with reasonable accuracy.

The relations between recombination rate and patterns of molecular variation and evolution in Drosophila.

Genetic recombination affects levels of variability and the efficacy of selection because natural selection acting at one site affects evolutionary processes at linked sites. The variation in local recombination rates across the Drosophila genome provides excellent material for testing hypotheses concerning the evolutionary consequences of recombination. The current state of knowledge from studies of Drosophila genomics and population genetics is reviewed here. Selection at linked sites has influenced the relations between recombination rates and patterns of molecular variation and evolution, such that higher rates of recombination are associated with both higher levels of variability and a greater efficacy of selection. It seems likely that background selection against deleterious mutations is a major factor contributing to these patterns in genome regions in which crossing over is rare or absent, whereas selective sweeps of positively selected mutations probably play an important role in regions with crossing over.

Effects of Selection at Linked Sites on Patterns of Genetic Variability.

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill-Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

Some complexities in interpreting apparent effects of hitchhiking: A commentary on Gompert et al. (2022).

We write to address recent claims by regarding the potentially important and underappreciated phenomena of "indirect selection," the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon-generally known as genetic hitchhiking-is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.

On the fixation or nonfixation of inversions under epistatic selection.

Several recent publications have stated that epistatic fitness interactions cause the fixation of inversions that suppress recombination among the loci involved. Under this type of selection, however, the suppression of recombination in an inversion heterozygote can create a form of heterozygote advantage, which prevents the inversion from becoming fixed by selection. This process has been explicitly modelled by previous workers.

How Long Does It Take to Fix a Favorable Mutation, and Why Should We Care?

The time taken for a selectively favorable allele to spread through a single population was investigated early in the history of population genetics. The resulting formulas are based on deterministic dynamics, leading to inaccuracies at allele frequencies close to 0 or 1. To remedy this problem, the properties of the stochastic phases at either end point of allele frequency need to be analyzed. This article uses a heuristic approach to determining the expected times spent in the stochastic and deterministic phases of allele frequency trajectories, for a model of weak selection at a single locus that is valid for inbreeding populations and for autosomal and sex-linked inheritance. The net fixation time is surprisingly insensitive to the level of dominance of a favorable mutation, even with random mating. Approximate expressions for the variance of the net fixation time are also obtained, which imply that there can be substantial stochastic effects even in very large populations. The accuracy of the approximations was evaluated by comparisons with computer simulations. The results reveal some areas that need further investigation if a full understanding of selective sweeps is to be obtained, notably the possibility that fixations of slightly deleterious mutations may be affecting variability at closely linked sites.

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion.

We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (πS ) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (KA ). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on πS and found that these could account for only part of the observed correlation between πS and KA We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high KA Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored.

Neutral Variation in the Context of Selection.

In its initial formulation by Motoo Kimura, the neutral theory was concerned solely with the level of variability maintained by random genetic drift of selectively neutral mutations, and the rate of molecular evolution caused by the fixation of such mutations. The original theory considered events at a single genetic locus in isolation from the rest of the genome. It did not take long, however, for theoreticians to wonder whether selection at one or more loci might influence neutral variability at linked sites. Once DNA sequence variability could be studied, and especially when resequencing of whole genomes became possible, it became clear that patterns of neutral variability in genomes are affected by selection at linked sites, and that these patterns could advance our understanding of natural selection, and can be used to detect the action of selection in genomic regions, including selection much weaker than could be detected by direct measurements of the relative fitnesses of different genotypes. We outline the different types of processes that have been studied, in approximate order of their historical development.

The Effects of Sex-Biased Gene Expression and X-Linkage on Rates of Sequence Evolution in Drosophila.

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant noncoding sequences of genes with different levels of sex-biased expression. Consistent with theory, nonsynonymous substitutions in most male-biased and unbiased genes show faster adaptive evolution on the X. However, genes with very low recombination rates do not show such an effect, possibly as a consequence of Hill-Robertson interference. Contrary to expectation, there was a substantial faster-X effect for female-biased genes. After correcting for recombination rate differences, however, female-biased genes did not show a faster X-effect. Similar analyses of noncoding UTRs and long introns showed a faster-X effect for all groups of genes, other than introns of female-biased genes. Given the strong evidence that deleterious mutations are mostly recessive or partially recessive, we would expect a slower rate of evolution of X-linked genes for slightly deleterious mutations that become fixed by genetic drift. Surprisingly, we found little evidence for this after correcting for recombination rate, implying that weakly deleterious mutations are mostly close to being semidominant. This is consistent with evidence from polymorphism data, which we use to test how models of selection that assume semidominance with no sex-specific fitness effects may bias estimates of purifying selection.

In defence of doing sums in genetics.

There has been a long history of the use of mathematics in genetics, ranging from the use of statistics to analyse genetic data to genetic models of evolutionary processes. Contemporary research into the genomic basis of disease and complex traits exemplifies the importance of statistical methods in genetics. Some examples of the development and application of population genetic models are described, which are intended to highlight the utility of such models for understanding variation and evolution in natural populations. The effects of selection on variability at sites linked to the targets of selection illustrate how fruitful interactions between theory and data can be.

Mutational load, inbreeding depression and heterosis in subdivided populations.

This paper examines the extent to which empirical estimates of inbreeding depression and interpopulation heterosis in subdivided populations, as well as the effects of local population size on mean fitness, can be explained in terms of current estimates of mutation rates, and the distribution of selection coefficients against deleterious mutations provided by population genomics data. Using population genetics models, numerical predictions of the genetic load, inbreeding depression and heterosis were obtained for a broad range of selection coefficients and mutation rates. The models allowed for the possibility of very high mutation rates per nucleotide site, as is sometimes observed for epiallelic mutations in plants. There was fairly good quantitative agreement between the theoretical predictions and empirical estimates of heterosis and the effects of population size on genetic load, on the assumption that the deleterious mutation rate per individual per generation is approximately one, but there was less good agreement for inbreeding depression. Weak selection, of the order of magnitude suggested by population genomic data, is required to explain the observed patterns. Possible caveats concerning the applicability of the models are discussed.

Faster-X evolution: Theory and evidence from Drosophila.

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes can be caused by the fixation of recessive or partially recessive advantageous mutations, due to the full expression of X-linked mutations in hemizygous males. Other processes, including recombination rate and mutation rate differences between X chromosomes and autosomes, may also cause faster evolution of X-linked genes. We review population genetics theory concerning the expected relative values of variability and rates of evolution of X-linked and autosomal DNA sequences. The theoretical predictions are compared with data from population genomic studies of several species of Drosophila. We conclude that there is evidence for adaptive faster-X evolution of several classes of functionally significant nucleotides. We also find evidence for potential differences in mutation rates between X-linked and autosomal genes, due to differences in mutational bias towards GC to AT mutations. Many aspects of the data are consistent with the male hemizygosity model, although not all possible confounding factors can be excluded.

Causes of natural variation in fitness: evidence from studies of Drosophila populations.

DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.

The sources of adaptive variation.

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

Industry-academic partnerships: an approach to accelerate innovation.

BACKGROUND: Biotechnology companies are process-driven organizations and often struggle with their ability to innovate. Universities, on the other hand, thrive on discovery and variation as a source of innovation. As such, properly structured academic-industry partnerships in medical technology development may enhance and accelerate innovation. Through joint industry-academic efforts, our objective was to develop a technology aimed at global cervical cancer prevention. METHODS: Our Center for Medical Innovation assembled a multidisciplinary team of students, surgical residents, and clinical faculty to enter in the University of Utah's annual Bench-to-Bedside competition. Bench-to-Bedside is a university program centered on medical innovation. Teams are given access to university resources and are provided $500.00 for prototype development. Participation by team members are on a volunteer basis. Our industry partner presented the validated need and business mentorship. The team studied the therapeutic landscape, environmental constraints, and used simulation to understand human factors design and usage requirements. A physical device was manufactured by first creating a digital image (SOLIDWORKS 3D CAD). Then, using a 3-dimensional printer (Stratasys Objet30 Prime 3D printer), the image was translated into a physical object. Tissue burn depth analysis was performed on raw chicken breasts warmed to room temperature. Varying combinations of time and temperature were tested, and burn depth and diameter were measured 30 min after each trial. An arithmetic mean was calculated for each corresponding time and temperature combination. User comprehension of operation and sterilization was tested via a participant validation study. Clinical obstetricians and gynecologists were given explicit instructions on usage details and then asked to operate the device. Participant behaviors and questions were recorded. RESULTS: Our efforts resulted in a functional battery-powered hand-held thermocoagulation prototype in just 72 d. Total cost of development was <$500. Proof of concept trials at 100°C demonstrated an average ablated depth and diameter of 4.7 mm and 23.3 mm, respectively, corresponding to treatment efficacy of all grades of precancerous cervical lesions. User comprehension studies showed variable understanding with respect to operation and sterilization instructions. CONCLUSIONS: Our experience with using industry-academic partnerships as a means to create medical technologies resulted in the rapid production of a low-cost device that could potentially serve as an integral piece of the "screen-and-treat" approach to premalignant cervical lesions as outlined by World Health Organization. This case study highlights the impact of accelerating medical advances through industry-academic partnership that leverages their combined resources.

Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys.

In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papionin monkeys (macaques, mangabeys, mandrills, drills, baboons, and geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To explore the potential genomic consequences of such sex differences, we used a reduced representation genome sequencing approach to quantifying polymorphism at sites on autosomes and sex chromosomes of the tonkean macaque (Macaca tonkeana), a species endemic to the Indonesian island of Sulawesi. The ratio of nucleotide diversity of the X chromosome to that of the autosomes was less than the value (0.75) expected with a 1:1 sex ratio and no sex differences in the variance in reproductive success. However, the significance of this difference was dependent on which outgroup was used to standardize diversity levels. Using a new model that includes the effects of varying population size, sex differences in mutation rate between the autosomes and X chromosome, and GC-biased gene conversion (gBGC) or selection on GC content, we found that the maximum-likelihood estimate of the ratio of effective population size of the X chromosome to that of the autosomes was 0.68, which did not differ significantly from 0.75. We also found evidence for 1) a higher level of purifying selection on genic than nongenic regions, 2) gBGC or natural selection favoring increased GC content, 3) a dynamic demography characterized by population growth and contraction, 4) a higher mutation rate in males than females, and 5) a very low polymorphism level on the Y chromosome. These findings shed light on the population genomic consequences of sex differences in the variance in reproductive success, which appear to be modest in the tonkean macaque; they also suggest the occurrence of hitchhiking on the Y chromosome.