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Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools. To fill this need we developed Apollo, a GPU-accelerated, out-of-core tool for within-host simulation of viral evolution and infection dynamics across population, tissue, and cellular levels. Apollo is scalable to hundreds of millions of viral genomes and can handle complex demographic and population genetic models. Apollo can replicate real within-host viral evolution; accurately recapturing observed viral sequences from an HIV cohort derived from initial population-genetic configurations. For practical applications, using Apollo-simulated viral genomes and transmission networks, we validated and uncovered the limitations of a widely used viral transmission inference tool.

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives., Competing Interests: COMPETING INTERESTS E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. C.T.W. is a co-founder/CSO of Clareo Biosciences, Inc. W.L. is a co-founder/CIO of Clareo Biosciences, Inc. The other authors declare no competing interests.

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations., Competing Interests: Conflicts of interest: The authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

qpAdm is a statistical tool that is often used in exploratory archaeogenetic studies for finding optimal admixture models of population history. Despite its popularity, qpAdm remains untested on histories in the form of admixture graphs of random topology or stepping-stone landscapes. We analyzed data from such simulations and found that while for admixture-graph-shaped histories there exist simple solutions (temporal stratification) for minimizing false findings of gene flow, in the case of stepping-stone landscapes the method generates results that do not appear suspect but are misleading: feasible qpAdm models are either accurate but simplistic in the context of landscapes, or highly inaccurate in the case of multi-component models. This is largely is due to two reasons: 1) because of complex migration networks that violate the assumptions of the method, there is poor correlation between qpAdm p -values and model optimality in many sections of the parameter space; 2) admixture fraction estimates between 0 and 1 are largely restricted to symmetric source configurations around targets, hence popular [0, 1] model plausibility criteria confound analyses of landscape-type demographies, unless their interpretations are explicitly spatial. For many species/regions/periods archaeogenetic sampling is very sparse and may be random with respect to population density of ancient individuals. In this situation only a specific combination of landscape properties and feasibility criteria allows to efficiently reject highly asymmetric non-optimal models most abundant in random deme sets. This problem may obscure useful signal (rare optimal models) and might be responsible for some claims about rapid long-distance migrations in the literature.

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility 1 . The X chromosome is vital for reproduction and cognition 2 . Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species., (© 2024. The Author(s).)

Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high-level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations. However, frameworks utilizing these features have not yet been compared and benchmarked. Here, we evaluate various simulation workflows using the coalescent simulator msprime and the forward simulator SLiM, to assess resource efficiency and determine an optimal simulation framework. Three aspects were evaluated: (1) the burn-in, to establish an equilibrium level of neutral diversity in the population; (2) the forward simulation, in which temporally fluctuating selection is acting; and (3) the final computation of summary statistics. We provide typical memory and computation time requirements for each step. We find that the fastest framework, a combination of coalescent and forward simulation with tree sequence recording, increases simulation speed by over twenty times compared to classical forward simulations without tree sequence recording, although it does require six times more memory. Overall, using efficient simulation workflows can lead to a substantial improvement when modelling complex evolutionary scenarios-although the optimal framework ultimately depends on the available computational resources., (© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson RR. In: Futuyma D, Antonovics J, editors. Gene genealogies and the coalescent process. In: Oxford Surveys in Evolutionary Biology; 1991. p. 1 to 44.). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches of those trees (Griffiths RC, Marjoram P. An ancestral recombination graph. In: Donnelly P, Tavare S, editors. Progress in population genetics and human evolution. Springer; 1997. p. 257 to 270.). Valuable insights can be gained into past evolutionary processes, such as demographic events or the influence of natural selection, by studying the ARG. It is regarded as the "holy grail" of population genetics (Hubisz M, Siepel A. Inference of ancestral recombination graphs using ARGweaver. In: Dutheil JY, editors. Statistical population genomics. New York, NY: Springer US; 2020. p. 231-266.) since it encodes the processes that generate all patterns of allelic and haplotypic variation from which all commonly used summary statistics in population genetic research (e.g. heterozygosity and linkage disequilibrium) can be derived. Many previous evolutionary inferences relied on summary statistics extracted from the genotype matrix. Evolutionary inferences using the ARG represent a significant advancement as the ARG is a representation of the evolutionary history of a sample that shows the past history of recombination, coalescence, and mutation events across a particular sequence. This representation in theory contains as much information, if not more, than the combination of all independent summary statistics that could be derived from the genotype matrix. Consistent with this idea, some of the first ARG-based analyses have proven to be more powerful than summary statistic-based analyses (Speidel L, Forest M, Shi S, Myers SR. A method for genome-wide genealogy estimation for thousands of samples. Nat Genet. 2019:51(9):1321 to 1329.; Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. PLoS Genet. 2019:15(9):e1008384.; Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet. 2020:16(8):e1008895.; Fan C, Mancuso N, Chiang CWK. A genealogical estimate of genetic relationships. Am J Hum Genet. 2022:109(5):812-824.; Fan C, Cahoon JL, Dinh BL, Ortega-Del Vecchyo D, Huber C, Edge MD, Mancuso N, Chiang CWK. A likelihood-based framework for demographic inference from genealogical trees. bioRxiv. 2023.10.10.561787. 2023.; Hejase HA, Mo Z, Campagna L, Siepel A. A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Mol Biol Evol. 2022:39(1):msab332.; Link V, Schraiber JG, Fan C, Dinh B, Mancuso N, Chiang CWK, Edge MD. Tree-based QTL mapping with expected local genetic relatedness matrices. bioRxiv. 2023.04.07.536093. 2023.; Zhang BC, Biddanda A, Gunnarsson ÁF, Cooper F, Palamara PF. Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nat Genet. 2023:55(5):768-776.). As such, there has been significant interest in the field to investigate 2 main problems related to the ARG: (i) How can we estimate the ARG based on genomic data, and (ii) how can we extract information of past evolutionary processes from the ARG? In this perspective, we highlight 3 topics that pertain to these main issues: The development of computational innovations that enable the estimation of the ARG; remaining challenges in estimating the ARG; and methodological advances for deducing evolutionary forces and mechanisms using the ARG. This perspective serves to introduce the readers to the types of questions that can be explored using the ARG and to highlight some of the most pressing issues that must be addressed in order to make ARG-based inference an indispensable tool for evolutionary research., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation., Competing Interests: Declaration of interests No interests are declared by the authors., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.

Repeated herbicide applications in agricultural fields exert strong selection on weeds such as blackgrass ( Alopecurus myosuroides ), which is a major threat for temperate climate cereal crops. This inadvertent selection pressure provides an opportunity for investigating the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much target-site resistance (TSR) relies on de novo mutations vs. standing variation is important for developing strategies to manage herbicide resistance. We first generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Next, through empirical data in the form of highly accurate long-read amplicons of alleles encoding acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS) variants, we showed that most populations with resistance due to TSR mutations-23 out of 27 and six out of nine populations for ACCase and ALS , respectively-contained at least two TSR haplotypes, indicating that soft sweeps are the norm. Finally, through forward-in-time simulations, we inferred that TSR is likely to mainly result from standing genetic variation, with only a minor role for de novo mutations.

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate., (© 2022. The Author(s).)

The potential biasing effect of irrelevant context information on the forensic odontology method of radiograph-based identification has never been empirically investigated despite being a recognized problem in other forensic science disciplines. This study examines the effect of irrelevant context information on the probability judgment of match (JOM) of practicing forensic odontologist and dentist participants who were asked to match pairs of dental radiographs supplemented with irrelevant case information. The irrelevant case information contained domain task-irrelevant context information which varied in strength (strong or weak). It suggested either supportive or contradictory bias relative to the actual match status of the radiograph pairs. The dental radiographs consisted of verified match and non-match radiographs pairs sampled and de-identified from actual forensic cases. Changes in accuracy and JOM between supportive and contradictory contexts conditions revealed a contextual bias. Mixed model analysis showed that strong supportive context increased the odds ratio of correct decisions by a factor of 2.4 [1.23, 4.46]; p = 0.0097. Consistent with the biasing effect, the JOM score differences between strong supportive and contradictory irrelevant context information were 1.03 and 0.43 respectively for the non-match and match decisions. The direction of context suggestion (p = 0.0067), the radiograph match status (p = 0.014), and their interactions (p = 0.0061), were all found to impact the participants' decision. The weak context information was not strong enough to have a significant effect on accuracy or JOM scores. This study demonstrates that radiograph match judgment is affected and can be biased by strong irrelevant contextual information., (Copyright © 2021 Elsevier B.V. All rights reserved.)

RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance). IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution., (Copyright © 2021 Dai et al.)

The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Quantifying and comparing the amount of adaptive evolution among different species is key to understanding how evolution works. Previous studies have shown differences in adaptive evolution across species; however, their specific causes remain elusive. Here, we use improved modeling of weakly deleterious mutations and the demographic history of the outgroup species and ancestral population and estimate that at least 20% of nonsynonymous substitutions between humans and an outgroup species were fixed by positive selection. This estimate is much higher than previous estimates, which did not correct for the sizes of the outgroup species and ancestral population. Next, we jointly estimate the proportion and selection coefficient ( p + and s + , respectively) of newly arising beneficial nonsynonymous mutations in humans, mice, and Drosophila melanogaster by examining patterns of polymorphism and divergence. We develop a novel composite likelihood framework to test whether these parameters differ across species. Overall, we reject a model with the same p + and s + of beneficial mutations across species and estimate that humans have a higher p + s + compared with that of D. melanogaster and mice. We show that this result cannot be caused by biased gene conversion or hypermutable CpG sites. We discuss possible biological explanations that could generate the observed differences in the amount of adaptive evolution across species., (© 2021 Zhen et al.; Published by Cold Spring Harbor Laboratory Press.)

Comparative genomic approaches have been used to identify sites where mutations are under purifying selection and of functional consequence by searching for sequences that are conserved across distantly related species. However, the performance of these approaches has not been rigorously evaluated under population genetic models. Further, short-lived functional elements may not leave a footprint of sequence conservation across many species. We use simulations to study how one measure of conservation, the Genomic Evolutionary Rate Profiling (GERP) score, relates to the strength of selection (Nes). We show that the GERP score is related to the strength of purifying selection. However, changes in selection coefficients or functional elements over time (i.e. functional turnover) can strongly affect the GERP distribution, leading to unexpected relationships between GERP and Nes. Further, we show that for functional elements that have a high turnover rate, adding more species to the analysis does not necessarily increase statistical power. Finally, we use the distribution of GERP scores across the human genome to compare models with and without turnover of sites where mutations are under purifying selection. We show that mutations in 4.51% of the noncoding human genome are under purifying selection and that most of this sequence has likely experienced changes in selection coefficients throughout mammalian evolution. Our work reveals limitations to using comparative genomic approaches to identify deleterious mutations. Commonly used GERP score thresholds miss over half of the noncoding sites in the human genome where mutations are under purifying selection., Competing Interests: The authors have declared that no competing interests exist.

In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism being controlled by a single genetic factor. Here, we use genome-wide pooled sequencing to explore the underlying genetic basis of bill morphology and identify a single candidate region. Targeted resequencing reveals extensive linkage disequilibrium across a 300 Kb region containing the insulin-like growth factor 1 (IGF1) gene, with a single 5-million-year-old haplotype associating with phenotypic dominance of the large-billed morph. We find no genetic similarities controlling bill size in the well-studied Darwin's finches (Geospiza). Our results show how a single genetic factor may control bill size and provide a foundation for future studies to examine this phenomenon within and among avian species.

Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16 th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate., (Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30-75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation., Competing Interests: The authors have declared that no competing interests exist.

Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, and complex traits. However, despite its importance, the degree of dominance in natural populations is poorly quantified. Here, we leverage multiple mating systems in natural populations of Arabidopsis to co-estimate the distribution of fitness effects and dominance coefficients of new amino acid changing mutations. We find that more deleterious mutations are more likely to be recessive than less deleterious mutations. Further, this pattern holds across gene categories, but varies with the connectivity and expression patterns of genes. Our work argues that dominance arises as a consequence of the functional importance of genes and their optimal expression levels.

The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fit∂a∂i, to estimate the DFE of new mutations using the site frequency spectrum from a large number of individuals. We apply our approach to the frequency spectrum of 1300 Europeans from the Exome Sequencing Project ESP6400 data set, 1298 Danes from the LuCamp data set, and 432 Europeans from the 1000 Genomes Project to estimate the DFE of deleterious nonsynonymous mutations. We infer significantly fewer (0.38-0.84 fold) strongly deleterious mutations with selection coefficient | s | > 0.01 and more (1.24-1.43 fold) weakly deleterious mutations with selection coefficient | s | < 0.001 compared to previous estimates. Furthermore, a DFE that is a mixture distribution of a point mass at neutrality plus a gamma distribution fits better than a gamma distribution in two of the three data sets. Our results suggest that nearly neutral forces play a larger role in human evolution than previously thought., (Copyright © 2017 by the Genetics Society of America.)

The distribution of fitness effects (DFE) of new mutations plays a fundamental role in evolutionary genetics. However, the extent to which the DFE differs across species has yet to be systematically investigated. Furthermore, the biological mechanisms determining the DFE in natural populations remain unclear. Here, we show that theoretical models emphasizing different biological factors at determining the DFE, such as protein stability, back-mutations, species complexity, and mutational robustness make distinct predictions about how the DFE will differ between species. Analyzing amino acid-changing variants from natural populations in a comparative population genomic framework, we find that humans have a higher proportion of strongly deleterious mutations than Drosophila melanogaster. Furthermore, when comparing the DFE across yeast, Drosophila , mice, and humans, the average selection coefficient becomes more deleterious with increasing species complexity. Last, pleiotropic genes have a DFE that is less variable than that of nonpleiotropic genes. Comparing four categories of theoretical models, only Fisher's geometrical model (FGM) is consistent with our findings. FGM assumes that multiple phenotypes are under stabilizing selection, with the number of phenotypes defining the complexity of the organism. Our results suggest that long-term population size and cost of complexity drive the evolution of the DFE, with many implications for evolutionary and medical genomics., Competing Interests: The authors declare no conflict of interest.

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation.

Unlabelled: SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map., Availability and Implementation: SweepFinder2 is a freely-available (www.personal.psu.edu/mxd60/sf2.html) software package that is written in C and can be run from a Unix command line., Contact: mxd60@psu.edu., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Objectives: Sinus augmentation is a standard procedure to increase vertical bone supply for dental implants in the atrophic posterior maxilla. Despite the longstanding application of this method, information about some basic factors that could potentially influence bone regeneration after sinus augmentation is rare. The objective of this study was therefore to quantify the impact of the maxillary region (premolar/molar) and patients' age and sex on bone regeneration after sinus grafting., Material and Methods: Sinus augmentation procedures were performed in 107 patients (66 female: 52.8 ± 11.0 years, 41 male: 50.6 ± 11.3 years). After 6 ± 1 months, 201 sinus biopsies were harvested and histomorphometrically analysed. Height (oldHt) and bone volume fraction of pristine bone (oldBV/TV), as well as the amount of new bone (newBV/TV) and bone-to-bone substitute contact (BBSC) in the augmentation area, were assessed., Results: In women, newBV/TV in the augmented sinus decreased significantly by 0.22 ± 0.08% per year. In men, no similar trend was observed. There were strong influences of the maxillary region and the dimensions of the host bone. In the premolar region, newBV/TV was 23.1 ± 7.9% and 25.1 ± 10.1%; in the molar region, newBV/TV averaged 20.4 ± 9.4% and 17.8 ± 8.8% for women and men, respectively. The greater the thickness of the wall of the sinus floor (mainly in the former premolar region), the greater was the amount of new bone tissue formed in the spaces in-between bone substitute particles., Conclusions: These empirical results derived from a large human sample, link factors that influence the quality of biomaterial integration to the known clinical risks for the success of dental implants., (© 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative to an out-group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone., (© 2015 John Wiley & Sons Ltd.)

Purpose: The study aims to evaluate the accuracy of the NobelGuide™ (Medicim/Nobel Biocare, Göteborg, Sweden) concept maximally reducing the influence of clinical and surgical parameters. Moreover, the study was to compare and validate two validation procedures versus a reference method., Material and Methods: Overall, 60 implants were placed in 10 artificial edentulous mandibles according to the NobelGuide™ protocol. For merging the pre- and postoperative DICOM data sets, three different fusion methods (Triple Scan Technique, NobelGuide™ Validation software, and AMIRA® software [VSG - Visualization Sciences Group, Burlington, MA, USA] as reference) were applied. Discrepancies between the virtual and the actual implant positions were measured., Results: The mean deviations measured with AMIRA® were 0.49 mm (implant shoulder), 0.69 mm (implant apex), and 1.98°mm (implant axis). The Triple Scan Technique as well as the NobelGuide™ Validation software revealed similar deviations compared with the reference method. A significant correlation between angular and apical deviations was seen (r = 0.53; p < .001). A greater implant diameter was associated with greater deviations (p = .03)., Conclusion: The Triple Scan Technique as a system-independent validation procedure as well as the NobelGuide™ Validation software are in accordance with the AMIRA® software. The NobelGuide™ system showed similar or less spatial and angular deviations compared with others., (© 2013 Wiley Periodicals, Inc.)

Detecting positive selection in species with heterogeneous habitats and complex demography is notoriously difficult and prone to statistical biases. The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found. Moreover, many aspects of the demography are unclear, which makes it hard to judge whether the few signals are indeed signs of selection, or false positives caused by demographic events. Here, we focus on Swedish A. thaliana and we find that the demography can be approximated as a two-population model. Careful analysis of the data shows that such a two island model is characterized by a very old split time that significantly predates the last glacial maximum followed by secondary contact with strong migration. We evaluate selection based on this demography and find that this secondary contact model strongly affects the power to detect sweeps. Moreover, it affects the power differently for northern Sweden (more false positives) as compared with southern Sweden (more false negatives). However, even when the demographic history is accounted for, sweep signals in northern Sweden are stronger than in southern Sweden, with little or no positional overlap. Further simulations including the complex demography and selection confirm that this is not compatible with global selection acting on both populations, and thus can be taken as evidence for local selection within subpopulations of Swedish A. thaliana. This study demonstrates the necessity of combining demographic analyses and sweep scans for the detection of selection, particularly when selection acts predominantly local., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Understanding how natural environments shape phenotypic variation is a major aim in evolutionary biology. Here, we have examined clinal, likely genetically based variation in morphology among 19 populations of the fruit fly (Drosophila melanogaster) from Africa and Europe, spanning a range from sea level to 3000 m altitude and including locations approximating the southern and northern range limit. We were interested in testing whether latitude and altitude have similar phenotypic effects, as has often been postulated. Both latitude and altitude were positively correlated with wing area, ovariole number, and cell number. In contrast, latitude and altitude had opposite effects on the ratio between ovariole number and body size, which was negatively correlated with egg production rate per ovariole. We also used transgenic manipulation to examine how increased cell number affects morphology and found that larger transgenic flies, due to a higher number of cells, had more ovarioles, larger wings, and, unlike flies from natural populations, increased wing loading. Clinal patterns in morphology are thus not a simple function of changes in body size; instead, each trait might be subject to different selection pressures. Together, our results provide compelling evidence for profound similarities as well as differences between phenotypic effects of latitude and altitude., (© 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.)

The major goal of evolutionary thermal biology is to understand how variation in temperature shapes phenotypic evolution. Comparing thermal reaction norms among populations from different thermal environments allows us to gain insights into the evolutionary mechanisms underlying thermal adaptation. Here, we have examined thermal adaptation in six wild populations of the fruit fly (Drosophila melanogaster) from markedly different natural environments by analyzing thermal reaction norms for fecundity, thorax length, wing area, and ovariole number under ecologically realistic fluctuating temperature regimes in the laboratory. Contrary to expectation, we found only minor differences in the thermal optima for fecundity among populations. Differentiation among populations was mainly due to differences in absolute (and partly also relative) thermal fecundity performance. Despite significant variation among populations in the absolute values of morphological traits, we observed only minor differentiation in their reaction norms. Overall, the thermal reaction norms for all traits examined were remarkably similar among different populations. Our results therefore suggest that thermal adaptation in D. melanogaster predominantly involves evolutionary changes in absolute trait values rather than in aspects of thermal reaction norms., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.

Purpose: The potential effect of Choukroun's platelet-rich fibrin (PRF) in combination with allograft on promoting bone regeneration has been discussed in previous publications. This study aims to evaluate an influence of PRF on bone regeneration in sinus augmentation in combination with a xenograft, deproteinised bovine bone., Materials and Methods: Eleven sinuses from 10 patients with posterior maxillary bone atrophy were selected for the study. As a test group, six sinus floor elevations were grafted with a Bio-Oss and PRF mixture, and as control group, five sinuses were treated with Bio-Oss alone. Clinical and radiographic examinations were performed pre- and postoperatively. After 6 months of sinus augmentation, bone biopsies were obtained from the grafted posterior maxilla, and un-decalcified ground sections were prepared. Bone characteristics were evaluated using histological observation and histomorphometric analyses., Results: No adverse effect was observed in any case within the follow-up period of 6 months after sinus augmentation. Histological observation showed similar morphological characteristics for both the PRF and control groups. The percentage of new bone formation in the PRF group was about 1.4 times of that in control (18.35%±5.62% vs. 12.95%±5.33%), while the percentage of residual bone substitute in the control group was about 1.5 times higher as that in the PRF group (28.54%±12.01% vs. 19.16%±6.89%). The percentage of contact length between newly formed bone and bone substitute in the PRF group was 21.45%±14.57% vs. 18.57%±5.39% in the control. No significant statistical differences between the two groups were found in these observed parameters., Conclusions: Our preliminary result demonstrated neither an advantage nor disadvantage of the application of PRF in combination with deproteinised bovine bone mineral in sinus augmentation after a healing period of 6 months., (Copyright © 2011 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)

Aim: Systemic bone loss is a major cause of fractures in postmenopausal women and may also affect the jawbone; however, its consequences on the success of dental implants remain poorly understood., Materials and Methods: In this cross-sectional study, the relation between self-reported osteoporosis and the success rate of dental implants in an adult female population was evaluated. The primary outcome parameters were the occurrence of peri-implantitis and late implant failures. Women with unknown bone status were excluded from the study. The potential confounders age, recipient site, smoking, periodontal disease and time of loading were recorded., Results: Data from 203 women with a mean age of 63 ± 9 years and 967 dental implants were investigated. The patients were classified according to their medical history into one of three groups: osteoporosis (47 women), osteopenia (16 women) and healthy controls (140 women). Patients with unknown bone status (n=26) were excluded. The multi-level statistical analysis showed no association between peri-implantitis [odds ratio (OR) 2.1; p=0.6] or implant failure [hazards ratio (HR) 2.5; p=0.2] and systemic bone loss., Conclusions: No relation was found between osteoporosis and peri-implantitis in an adult female population., (© 2011 John Wiley & Sons A/S.)

Objective: Pseudoaneurysms are characterized by extravascular circulation and therefore may lead to an activation of the coagulation cascade. We investigated d-dimer levels in patients with and without postcatheterization femoral pseudoaneurysms and hypothesized that d-dimer levels correlate with the presence of pseudoaneurysms at the vascular access site., Methods: Patients with clinical suspected groin pseudoaneurysms after transluminal procedures were eligible. We compared prospectively-collected laboratory values of quantitative d-dimer testing in patients with and without pseudoaneurysms as assessed by color-coded duplex sonography. Furthermore, we measured the peak systolic velocity at the arterial fistula of each pseudoaneurysm., Results: In 48 (40%) of 120 consecutive patients, a pseudoaneurysm was found. The level of d-dimer values was significantly higher in patients with postcatheterization femoral pseudoaneurysms compared with controls (1.9 microg/mL [interquartile range (IQR), 1.34-2.78 microg/mL] vs 0.8 microg/mL [IQR, 0.53-1.14 microg/mL]; P < .001). Values of d-dimer below 0.67 microg/mL have been calculated with a sensitivity of 94% (87%-100%), a specificity of 38% (27%-50%), a positive predictive value of 50% (40%-60%), a negative predictive value of 90% (82%-99%), and a likelihood ratio of 1.52 (1.25-1.85) with regard to the presence of pseudoaneurysms. We also found a significant correlation of the peak systolic velocity at the arterial fistula and increasing d-dimer levels (r = 0.98, P < .0001)., Conclusion: We found a significantly higher level of d-dimer values in patients with femoral pseudoaneurysms at the vascular access site. Therefore, d-dimer levels could be a potential serological marker in the diagnosis of pseudoaneurysms. A confirmation is warranted in a larger patient sample., (Copyright (c) 2010 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.)

Objective: Graft consolidation follows a gradient that reflects the properties of bone substitutes at sites of sinus augmentation. Here we present an analytical method to investigate the process of graft consolidation taking the distance from the maxillary host bone into account., Material and Methods: We therefore evaluated histological specimens, 6 and 12 weeks after the sinus of minipigs was augmented with Bio-Oss((R)), a deproteinized bovine bone mineral, and Ostim((R)), an aqueous paste of synthetic nanoparticular hydroxyapatite. A curve was drawn that represents the changes in histomorphometric parameters within a given distance from the maxillary host bone., Results: Based on this curve, three regions of interest were defined: R1 (0-1 mm) the bridging distance where new bone is laid onto the host bone, R2 (2-3 mm) a region of osteoconduction where new bone exclusively grows on the biomaterial, R3 (4-5 mm) and a region of osteoconduction where bone formation has reached its maximal extension. Qualitative and quantitative analysis of the three regions can reveal differences in graft consolidation, depending on the bone substitutes and the observation period [Bone volume (BV) per tissue volume after 6 weeks: R1: 19+/-8.4% for Bio-Oss((R)) and 42.9+/-13.2% for Ostim((R)) (P=0.03), R2: 3+/-2.4% for Bio-Oss((R)) and 14.7+/-9.5% for Ostim((R)) (P=0.03), R3: 5+/-4.1% for Bio-Oss((R)) and 5.3+/-5.3% for Ostim((R)) (P=0.86). BV per tissue volume after 12 weeks: R1: 38.0+/-13.3% for Bio-Oss((R)) and 53.3+/-6.6 for Ostim((R)) (P=0.04), R2: 14+/-12.2 for Bio-Oss((R)) and 26.4+/-11 for Ostim((R)) (P=0.18), R3: 6.6+/-7 for Bio-Oss((R)) and 10.7+/-5.8 for Ostim((R)) (P=0.32) after 12 weeks]., Conclusion: Based on the graft consolidation gradient, the impact of bone substitutes to modulate the process of bone formation and the kinetic of degradation within a distinct region of the augmented sinus can be investigated.

A finite element (FE) model of a 10-years-old child pelvis was developed and validated against experimental data from lateral impacts of pediatric pelves. The pelvic bone geometry was reconstructed from a set of computed tomography images, and a hexahedral mesh was generated using a new octree-based hexahedral meshing technique. Lateral impacts to the greater trochanter and iliac wing of the seated pelvis were simulated. Sensitivity analysis was conducted to identify material parameters that substantially affected the model response. An optimization-based material identification method was developed to obtain the most favorable material property set by minimizing differences in biomechanical responses between experimental and simulation results. This study represents a pilot effort in the development and validation of age-dependent musculoskeletal FE models for children, which may ultimately serve to evaluate injury mechanisms and means of protection for the pediatric population.

The edentulous ovine diastema represents a suitable region for implantological research. Due to distinctive embryonic origin and mechanical loading, the edentulous diastema may respond differently to osteoporosis than tooth-bearing areas. To test this assumption, we subjected geriatric sheep to ovariectomy, calcium-/vitamin-D-restricted diet, and methylprednisolone administration. Adult control sheep remained untreated. Structural parameters and bone mineral density were determined by microcomputed tomography and conventional computed tomography, respectively. We report that the trabecular microstructure in the diastema was preserved from catabolic changes. In contrast, the premolar maxillary region of osteoporotic sheep had diminished trabecular bone mineral density, with the corresponding structural deteriorations. These results suggest that maxillary trabecular bone of the edentulous diastema does not respond to catabolic changes which occur in the tooth-bearing area in osteoporosis. Our findings imply that regional anatomic domains must be considered in the planning of pre-clinical studies, taking osteoporotic changes into account.

The aim of the present study was to compare the accuracy, precision, and bias of two macroscopic and one histological age at death estimation methods on human teeth. The sample was comprised of 67 permanent teeth, obtained from 37 individuals aged 20-91 years. Age was predicted according to the methods proposed by Lamendin et al. (LAM), Bang and Ramm (BR), and the quantification of tooth cementum annulations (TCA). TCA was found to be most accurate in all age groups. Its mean absolute error of the estimated age was about half as high as the mean absolute error for both LAM and BR. BR achieved approximately the same mean absolute error as TCA for old adults only. LAM displayed the highest precision in the young and the old age group whereas TCA was more precise in the middle age group. TCA was found to be the most precise method when the precision was calculated for all ages. Considering the bias, all methods displayed a tendency to overestimate age in young and to underestimate it in old specimens. The exception to this rule was TCA, which provided unbiased estimates for young adults. The higher accuracy and precision recommends favouring TCA over LAM and BR, provided that the required know-how and equipment are available.

Objectives: Safety of the airbag supplemental restraint system (airbag) is a well-known concern. Although many lives are saved each year through airbag use, injuries continue to occur, especially to the head. Airbag safety research has focused primarily on severe injuries, while minor and moderate injuries have been largely ignored., Methods: In this study, 205,977 injury cases from the 1995 to 2001 National Automotive Sampling System (NASS)/ Crashworthiness Data System (CDS) were surveyed to determine the prevalence of AIS 1 and 2 facial and brain loss of consciousness (LOC) injuries and determine if these injuries are a concern. The query was focused on frontal impacts in vehicles equipped with airbags. Only occupants wearing appropriate seatbelts were included in this study so that the airbag would provide occupant protection under optimal conditions. Of the 205,977 injury cases studied, 2.4% met this criterion., Results: From the data gathered, the trends seem to indicate an increase in these specific injuries, both in terms of the total number and the proportion to all injury cases. In 1995, AIS 1 and 2 head injuries accounted for 96.5% of all head injuries caused by airbags. By 2001, the percentage had risen 3.0% to 99.5%. Injuries occurring in vehicles equipped with first-generation versus second generation airbags were compared, and data seem to suggest that there is a higher rate of minor and moderate head injuries when occupants are in second-generation airbag-equipped vehicles, even when appropriate lap and shoulder belts are used., Conclusions: The short timeframe surveyed prevents drawing meaningful conclusions about statistical significance, but the graphical representations of the data in this study underscore an urgent need for further investigation based on current trends in order to understand the issue of minor and moderate head injury prevention in regard to airbags.