Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster

Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution

For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins.

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

The piRNA pathway is a highly conserved mechanism to repress transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster with high-quality long-read genome assemblies. We perform annotations of ovary piCs and genome-wide TE content in each strain. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions into old and large piCs, consistent with the previously proposed "trap" model of piC evolution. In contrast, a small subset of active LTR families is enriched for the formation of new piCs, suggesting that these TEs have higher proclivity to form piCs. Thus, our findings uncover processes leading to the origin of piCs. We propose that piC evolution begins with the emergence of piRNAs from individual insertions of a few select TE families prone to seed new piCs that subsequently expand by accretion of insertions from most other TE families during evolution to form larger "trap" clusters. Our study shows that TEs themselves are the major force driving the rapid evolution of piCs.

A general and efficient representation of ancestral recombination graphs

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. This approach is out of step with modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalises these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.

Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations

Simulations are an essential tool in all areas of population genetic research, used in tasks such as the validation of theoretical analysis and the study of complex evolutionary models. Forward-in-time simulations are especially flexible, allowing for various types of natural selection, complex genetic architectures, and non-Wright-Fisher dynamics. However, their intense computational requirements can be prohibitive to simulating large populations and genomes. A popular method to alleviate this burden is to scale down the population size by some scaling factor while scaling up the mutation rate, selection coefficients, and recombination rate by the same factor. However, this rescaling approach may in some cases bias simulation results. To investigate the manner and degree to which rescaling impacts simulation outcomes, we carried out simulations with different demographic histories and distributions of fitness effects using several values of the rescaling factor, Q , and compared the deviation of key outcomes (fixation times, fixation probabilities, allele frequencies, and linkage disequilibrium) between the scaled and unscaled simulations. Our results indicate that scaling introduces substantial biases to each of these measured outcomes, even at small values of Q . Moreover, the nature of these effects depends on the evolutionary model and scaling factor being examined. While increasing the scaling factor tends to increase the observed biases, this relationship is not always straightforward, thus it may be difficult to know the impact of scaling on simulation outcomes a priori. However, it appears that for most models, only a small number of replicates was needed to accurately quantify the bias produced by rescaling for a given Q . In summary, while rescaling forward-in-time simulations may be necessary in many cases, researchers should be aware of the rescaling effect's impact on simulation outcomes and consider investigating its magnitude in smaller scale simulations of the desired model(s) before selecting an appropriate value of Q .

Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species

The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.

Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection

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.

Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes

Anopheles gambiae s.l. has been the target of intense insecticide treatment since the mid-20th century to try and control malaria. A substitution in the ace-1 locus has been rapidly selected for, allowing resistance to organophosphate and carbamate insecticides. Since then, two types of duplication of the ace-1 locus have been found in An. gambiae s.l. populations: homogeneous duplications that are composed of several resistance copies, or heterogeneous duplications that contain both resistance and susceptible copies. The substitution induces a trade-off between resistance in the presence of insecticides and disadvantages in their absence: the heterogeneous duplications allow the fixation of the intermediate heterozygote phenotype. So far, a single heterogeneous duplication has been described in An. gambiae s.l. populations (in contrast with the multiple duplicated alleles found in Culex pipiens mosquitoes). We used a new approach, combining long and short-read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications, in two populations of An. gambiae s.l. We show that these alleles share the same structure as the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds new light on the origin and maintenance of these alleles in An. gambiae s.l. populations, and their role in mosquito adaptation.

Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species

The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.

Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird

Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.

The divergence of mutation rates and spectra across the Tree of Life

Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.

The Contribution of Mutation to Variation in Temperature-Dependent Sprint Speed in Zebrafish, Danio rerio

AbstractThe contribution of new mutations to phenotypic variation and the consequences of this variation for individual fitness are fundamental concepts for understanding genetic variation and adaptation. Here, we investigated how mutation influenced variation in a complex trait in zebrafish, Danio rerio. Typical of many ecologically relevant traits in ectotherms, swimming speed in fish is temperature dependent, with evidence of adaptive evolution of thermal performance. We chemically induced novel germline point mutations in males and measured sprint speed in their sons at six temperatures (between 16°C and 34°C). Heterozygous mutational effects on speed were strongly positively correlated among temperatures, resulting in statistical support for only a single axis of mutational variation, reflecting temperature-independent variation in speed (faster-slower mode). These results suggest pleiotropic effects on speed across different temperatures; however, spurious correlations arise via linkage or heterogeneity in mutation number when mutations have consistent directional effects on each trait. Here, mutation did not change mean speed, indicating no directional bias in mutational effects. The results contribute to emerging evidence that mutations may predominantly have synergistic cross-environment effects, in contrast to conditionally neutral or antagonistic effects that underpin thermal adaptation. We discuss several aspects of experimental design that may affect resolution of mutations with nonsynergistic effects.

Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis

Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.

Low Spontaneous Mutation Rate in Complex Multicellular Eukaryotes with a Haploid-Diploid Life Cycle

The spontaneous mutation rate µ is a crucial parameter to understand evolution and biodiversity. Mutation rates are highly variable across species, suggesting that µ is susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect the mutation rate, but very little empirical data are available to test this expectation. Here, we sequence 30 genomes of a parent-offspring pedigree in the model brown alga Ectocarpus sp.7, and 137 genomes of an interspecific cross of the closely related brown alga Scytosiphon to have access to the spontaneous mutation rate of representative organisms of a complex multicellular eukaryotic lineage outside animals and plants, and to evaluate the potential impact of life cycle on the mutation rate. Brown algae alternate between a haploid and a diploid stage, both multicellular and free living, and utilize both sexual and asexual reproduction. They are, therefore, excellent models to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate that Ectocarpus has a base substitution rate of µbs = 4.07 × 10-10 per site per generation, whereas the Scytosiphon interspecific cross had µbs = 1.22 × 10-9. Overall, our estimations suggest that these brown algae, despite being multicellular complex eukaryotes, have unusually low mutation rates. In Ectocarpus, effective population size (Ne) could not entirely explain the low µbs. We propose that the haploid-diploid life cycle, combined with extensive asexual reproduction, may be additional key drivers of the mutation rate in these organisms.

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

Animal genomes are parasitized by a horde of transposable elements (TEs) whose mutagenic activity can have catastrophic consequences. The piRNA pathway is a conserved mechanism to repress TE activity in the germline via a specialized class of small RNAs associated with effector Piwi proteins called piwi-associated RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). While piCs are generally enriched for TE sequences and the molecular processes by which they are transcribed and regulated are relatively well understood in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC evolution, we use a population genomics approach to compare piC activity and sequence composition across 8 geographically distant strains of D. melanogaster with high quality long-read genome assemblies. We perform extensive annotations of ovary piCs and TE content in each strain and test predictions of two proposed models of piC evolution. The 'de novo' model posits that individual TE insertions can spontaneously attain the status of a small piC to generate piRNAs silencing the entire TE family. The 'trap' model envisions large and evolutionary stable genomic clusters where TEs tend to accumulate and serves as a long-term "memory" of ancient TE invasions and produce a great variety of piRNAs protecting against related TEs entering the genome. It remains unclear which model best describes the evolution of piCs. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs in natural populations. Most TE families inferred to be recently or currently active show an enrichment of strain-specific insertions into large piCs, consistent with the trap model. By contrast, only a small subset of active LTR retrotransposon families is enriched for the formation of strain-specific piCs, suggesting that these families have an inherent proclivity to form de novo piCs. Thus, our findings support aspects of both 'de novo' and 'trap' models of piC evolution. We propose that these two models represent two extreme stages along an evolutionary continuum, which begins with the emergence of piCs de novo from a few specific LTR retrotransposon insertions that subsequently expand by accretion of other TE insertions during evolution to form larger 'trap' clusters. Our study shows that piCs are evolutionarily labile and that TEs themselves are the major force driving the formation and evolution of piCs.

Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such as Drosophila melanogaster and Drosophila simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge of this variation is fundamental for parameterizing models of genome evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans Across 89 flies, we observe 58 single-nucleotide mutations, 286 crossovers, and 89 transposable element (TE) insertions. Compared to the European D. melanogaster, we find the West African population has a lower mutation rate (1.67 × 10-9 site-1 gen-1 vs. 4.86 × 10-9 site-1 gen-1) and a lower transposition rate (8.99 × 10-5 copy-1 gen-1 vs. 23.36 × 10-5 copy-1 gen-1), but a higher recombination rate (3.44 cM/Mb vs. 2.06 cM/Mb). The European D. simulans population has a similar mutation rate to European D. melanogaster, but a significantly higher recombination rate and a lower, but not significantly different, transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimates of these parameters in D. melanogaster and D. simulans will benefit future studies in population and evolutionary genetics.

The genetic architecture of behavioral canalization

Behaviors are components of fitness and contribute to adaptive evolution. Behaviors represent the interactions of an organism with its environment, yet innate behaviors display robustness in the face of environmental change, which we refer to as 'behavioral canalization'. We hypothesize that positive selection of hub genes of genetic networks stabilizes the genetic architecture for innate behaviors by reducing variation in the expression of interconnected network genes. Robustness of these stabilized networks would be protected from deleterious mutations by purifying selection or suppressing epistasis. We propose that, together with newly emerging favorable mutations, epistatically suppressed mutations can generate a reservoir of cryptic genetic variation that could give rise to decanalization when genetic backgrounds or environmental conditions change to allow behavioral adaptation.

Interrogating the Roles of Mutation-Selection Balance, Heterozygote Advantage, and Linked Selection in Maintaining Recessive Lethal Variation in Natural Populations

For nearly a century, evolutionary biologists have observed chromosomes that cause lethality when made homozygous persisting at surprisingly high frequencies (>25%) in natural populations of many species. The evolutionary forces responsible for the maintenance of such detrimental mutations have been heavily debated-are some lethal mutations under balancing selection? We suggest that mutation-selection balance alone cannot explain lethal variation in nature and the possibility that other forces play a role. We review the potential that linked selection in particular may drive maintenance of lethal alleles through associative overdominance or linkage to beneficial mutations or by reducing effective population size. Over the past five decades, investigation into this mystery has tapered. During this time, key scientific advances have provided the ability to collect more accurate data and analyze them in new ways, making the underlying genetic bases and evolutionary forces of lethal alleles timely for study once more.

Variation in mutational (co)variances

Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode Caenorhabditis elegans that accumulated mutations in a nearly neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of C. elegans genotypes allows selection on new phenotypic dimensions of locomotion behavior.

Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum

The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate. In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum, a eukaryote with among the lowest point mutation rates (2.5 × 10-11 per site per generation) and an AT-rich genome (GC content of 22%). We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10-8 gene deletions and 1.18 × 10-8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10-6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.

GADMA2: more efficient and flexible demographic inference from genetic data

BACKGROUND

Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm.

RESULTS

Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm, and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data, and demonstrate an example of GADMA2 usage on 2 empirical datasets.

CONCLUSIONS

We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2's likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for 2 empirical datasets of inbred species.

Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution?

Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.

Genomic Analyses Implicate the Amazon-Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

The Amazon-Orinoco plume (AOP) is the world's largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP's formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.

Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukii

Engineered Genetic Incompatibility (EGI) is an engineered extreme underdominance genetic system wherein hybrid animals are not viable, functioning as a synthetic speciation event. There are several strategies in which EGI could be leveraged for genetic biocontrol of pest populations. We used an agent-based model of Drosophila suzukii (Spotted Wing Drosophila) to determine how EGI would fare with high rates of endemic genetic resistance alleles. We discovered a surprising failure mode wherein field-generated females convert an incompatible male release program into a population replacement gene drive. Local suppression could still be attained in two seasons by tailoring the release strategy to take advantage of this effect, or alternatively in one season by altering the genetic design of release agents. We show in this work that data from modeling can be utilized to recognize unexpected emergent phenomena and a priori inform genetic biocontrol treatment design to increase efficacy.

Adaptive evolvability through direct selection instead of indirect, second-order selection

Can evolvability itself be the product of adaptive evolution? To answer this question is challenging, because any DNA mutation that alters only evolvability is subject to indirect, "second order" selection on the future effects of this mutation. Such indirect selection is weaker than "first-order" selection on mutations that alter fitness, in the sense that it can operate only under restrictive conditions. Here I discuss a route to adaptive evolvability that overcomes this challenge. Specifically, a recent evolution experiment showed that some mutations can enhance both fitness and evolvability through a combination of direct and indirect selection. Unrelated evidence from gene duplication and the evolution of gene regulation suggests that mutations with such dual effects may not be rare. Through such mutations, evolvability may increase at least in part because it provides an adaptive advantage. These observations suggest a research program on the adaptive evolution of evolvability, which aims to identify such mutations and to disentangle their direct fitness effects from their indirect effects on evolvability. If evolvability is itself adaptive, Darwinian evolution may have created more than life's diversity. It may also have helped create the very conditions that made the success of Darwinian evolution possible.

Selection in a growing colony biases results of mutation accumulation experiments

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 10⁸). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

Causes of variability in estimates of mutational variance from mutation accumulation experiments

Characteristics of the new phenotypic variation introduced via mutation have broad implications in evolutionary and medical genetics. Standardized estimates of this mutational variance, V_M, span 2 orders of magnitude, but the causes of this remain poorly resolved. We investigated estimate heterogeneity using 2 approaches. First, meta-analyses of ∼150 estimates of standardized V_M from 37 mutation accumulation studies did not support a difference among taxa (which differ in mutation rate) but provided equivocal support for differences among trait types (life history vs morphology, predicted to differ in mutation rate). Notably, several experimental factors were confounded with taxon and trait, and further empirical data are required to resolve their influences. Second, we analyzed morphological data from an experiment in Drosophila serrata to determine the potential for unintentional heterogeneity among environments in which phenotypes were measured (i.e. among laboratories or time points) or transient segregation of mutations within mutation accumulation lines to affect standardized V_M. Approximating the size of an average mutation accumulation experiment, variability among repeated estimates of (accumulated) mutational variance was comparable to variation among published estimates of standardized V_M. This heterogeneity was (partially) attributable to unintended environmental variation or within line segregation of mutations only for wing size, not wing shape traits. We conclude that sampling error contributed substantial variation within this experiment, and infer that it will also contribute substantially to differences among published estimates. We suggest a logistically permissive approach to improve the precision of estimates, and consequently our understanding of the dynamics of mutational variance of quantitative traits.

Genetic Signatures from Adaptation of Bacteria to Lytic Phage Identify Potential Agents to Aid Phage-Killing of Multidrug-Resistant Acinetobacter baumannii

With the increasing morbidity and mortality rates associated with multidrug-resistant bacteria, interest in bacteriophage therapy has been revived. However, bacterial resistance to phage infection threatens the usefulness of phage therapy, especially its inclusion in modern medicine. Multidrug-resistant Acinetobacter baumannii is a top priority pathogen requiring urgent intervention and new therapeutic approaches, such as phage therapy. Here, we experimentally adapted A. baumannii WHG40004 to its lytic phage P21, and thereafter isolated a phage-resistant bacterial mutant, named Ev5-WHG. We then aimed to identify potential agents to aid phage-killing of Ev5-WHG by analyzing its genome and that of the wildtype strain. The enriched Gene Ontology (GO) analysis based on genetic alterations in minor alleles and mutations showed that pathways such as zinc ion transport and cell membrane synthesis could play certain roles in phage resistance. Remarkably, the combination of zinc acetate and P21 showed increased bactericidal effect on Ev5-WHG. Significantly also, we showed that P21 completely prevented the growth of wildtype WHG40004 in the presence of antibiotics (meropenem and imipenem). The results from this study indicate that the analysis of phage resistance signatures during adaptation of bacteria to a lytic phage can inform choice of agents to work cooperatively with phage to limit and/or reverse resistance. This approach could be important for guiding future successful phage therapy. Importance Bacteriophages have proven very useful as alternative therapeutic agents in combating multidrug-resistant bacterial infections, however, bacterial resistance to phages threatens their use. In this study, we showed a new strategy of leveraging on genetic signatures that accompany phage resistance in bacteria to predict agents that can be used with lytic phages to combat multidrug-resistant Acinetobacter baumannii. Significantly, this approach was helpful in suggesting the use of zinc acetate to reduce resistance in phage-resistant bacteria, as well as the use of phage with antibiotics meropenem and imipenem to prevent resistance in wildtype strain of MDR A. baumannii. The approach of this study will be helpful for improving the outcome of phage therapy and in overcoming antimicrobial resistance.

KNNCNV: A K-Nearest Neighbor Based Method for Detection of Copy Number Variations Using NGS Data

Copy number variation (CNV) is a well-known type of genomic mutation that is associated with the development of human cancer diseases. Detection of CNVs from the human genome is a crucial step for the pipeline of starting from mutation analysis to cancer disease diagnosis and treatment. Next-generation sequencing (NGS) data provides an unprecedented opportunity for CNVs detection at the base-level resolution, and currently, many methods have been developed for CNVs detection using NGS data. However, due to the intrinsic complexity of CNVs structures and NGS data itself, accurate detection of CNVs still faces many challenges. In this paper, we present an alternative method, called KNNCNV (K-Nearest Neighbor based CNV detection), for the detection of CNVs using NGS data. Compared to current methods, KNNCNV has several distinctive features: 1) it assigns an outlier score to each genome segment based solely on its first k nearest-neighbor distances, which is not only easy to extend to other data types but also improves the power of discovering CNVs, especially the local CNVs that are likely to be masked by their surrounding regions; 2) it employs the variational Bayesian Gaussian mixture model (VBGMM) to transform these scores into a series of binary labels without a user-defined threshold. To evaluate the performance of KNNCNV, we conduct both simulation and real sequencing data experiments and make comparisons with peer methods. The experimental results show that KNNCNV could derive better performance than others in terms of F1-score.

Adaptation dynamics between copy-number and point mutations

Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.

Intraspecific Variation in the Rates of Mutations Causing Structural Variation in Daphnia magna

Mutations that cause structural variation are important sources of genetic variation upon which other evolutionary forces can act, however, they are difficult to observe and therefore few direct estimates of their rate and spectrum are available. Understanding mutation rate evolution, however, requires adding to the limited number of species for which direct estimates are available, quantifying levels of intraspecific variation in mutation rates, and assessing whether rate estimates co-vary across types of mutation. Here, we report structural variation-causing mutation rates (svcMRs) for six categories of mutations (short insertions and deletions, long deletions and duplications, and deletions and duplications at copy number variable sites) from nine genotypes of Daphnia magna collected from three populations in Finland, Germany, and Israel using a mutation accumulation approach. Based on whole-genome sequence data and validated using simulations, we find svcMRs are high (two orders of magnitude higher than base substitution mutation rates measured in the same lineages), highly variable among populations, and uncorrelated across categories of mutation. Furthermore, to assess the impact of scvMRs on the genome, we calculated rates while adjusting for the lengths of events and ran simulations to determine if the mutations occur in genic regions more or less frequently than expected by chance. Our results pose a challenge to most prevailing theories aimed at explaining the evolution of the mutation rate, underscoring the importance of obtaining additional mutation rate estimates in more genotypes, for more types of mutation, in more species, in order to improve our future understanding of mutation rates, their variation, and their evolution.

Protein innovation through template switching in the Saccharomyces cerevisiae lineage

DNA polymerase template switching between short, non-identical inverted repeats (IRs) is a genetic mechanism that leads to the homogenization of IR arms and to IR spacer inversion, which cause multinucleotide mutations (MNMs). It is unknown if and how template switching affects gene evolution. In this study, we performed a phylogenetic analysis to determine the effect of template switching between IR arms on coding DNA of Saccharomyces cerevisiae. To achieve this, perfect IRs that co-occurred with MNMs between a strain and its parental node were identified in S. cerevisiae strains. We determined that template switching introduced MNMs into 39 protein-coding genes through S. cerevisiae evolution, resulting in both arm homogenization and inversion of the IR spacer. These events in turn resulted in nonsynonymous substitutions and up to five neighboring amino acid replacements in a single gene. The study demonstrates that template switching is a powerful generator of multiple substitutions within codons. Additionally, some template switching events occurred more than once during S. cerevisiae evolution. Our findings suggest that template switching constitutes a general mutagenic mechanism that results in both nonsynonymous substitutions and parallel evolution, which are traditionally considered as evidence for positive selection, without the need for adaptive explanations.

The genome-wide rate and spectrum of EMS-induced heritable mutations in the microcrustacean Daphnia: on the prospect of forward genetics

Forward genetic screening using the alkylating mutagen ethyl methanesulfonate (EMS) is an effective method for identifying phenotypic mutants of interest, which can be further genetically dissected to pinpoint the causal genetic mutations. An accurate estimate of the rate of EMS-induced heritable mutations is fundamental for determining the mutant sample size of a screening experiment that aims to saturate all the genes in a genome with mutations. This study examines the genome-wide EMS-induced heritable base-substitutions in three species of the freshwater microcrustacean Daphnia to help guide screening experiments. Our results show that the 10 mM EMS treatment induces base substitutions at an average rate of 1.17 × 10^-6/site/generation across the three species, whereas a significantly higher average mutation rate of 1.75 × 10^-6 occurs at 25 mM. The mutation spectrum of EMS-induced base substitutions at both concentration is dominated by G:C to A:T transitions. Furthermore, we find that female Daphnia exposed to EMS (F₀ individuals) can asexually produce unique mutant offspring (F₁) for at least 3 consecutive broods, suggestive of multiple broods as F₁ mutants. Lastly, we estimate that about 750 F₁s are needed for all genes in the Daphnia genome to be mutated at least once with a 95% probability. We also recommend 4-5 F₂s should be collected from each F₁ mutant through sibling crossing so that all induced mutations could appear in the homozygous state in the F₂ population at 70-80% probability.

Amplicon remodeling and genomic mutations drive population dynamics after segmental amplification

New enzymes often evolve by duplication and divergence of genes encoding enzymes with promiscuous activities that have become important in the face of environmental opportunities or challenges. Amplifications that increase the copy number of the gene under selection commonly amplify many surrounding genes. Extra copies of these coamplified genes must be removed, either during or after evolution of a new enzyme. Here we report that amplicon remodeling can begin even before mutations occur in the gene under selection. Amplicon remodeling and mutations elsewhere in the genome that indirectly increase fitness result in complex population dynamics, leading to emergence of clones that have improved fitness by different mechanisms. In this work, one of the two most successful clones had undergone two episodes of amplicon remodeling, leaving only four coamplified genes surrounding the gene under selection. Amplicon remodeling in the other clone resulted in removal of 111 genes from the genome, an acceptable solution under these selection conditions, but one that would certainly impair fitness under other environmental conditions.

Temperature dependence of spontaneous mutation rates

Mutation is the source of genetic variation and the fundament of evolution. Temperature has long been suggested to have a direct impact on realized spontaneous mutation rates. If mutation rates vary in response to environmental conditions, such as the variation of the ambient temperature through space and time, they should no longer be described as species-specific constants. By combining mutation accumulation with whole-genome sequencing in a multicellular organism, we provide empirical support to reject the null hypothesis of a constant, temperature-independent mutation rate. Instead, mutation rates depended on temperature in a U-shaped manner with increasing rates toward both temperature extremes. This relation has important implications for mutation-dependent processes in molecular evolution, processes shaping the evolution of mutation rates, and even the evolution of biodiversity as such.

No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals

Nested protein-coding genes accumulated throughout metazoan evolution, with early analyses of human and Drosophila microarray data indicating that this phenomenon was simply due to the presence of large introns. However, a recent study employing RNA-seq data uncovered evidence of transcriptional interference driving rapid expression divergence between Drosophila nested genes, illustrating that accurate expression estimation of overlapping genes can enhance detection of their relationships. Hence, here I apply an analogous approach to strand-specific RNA-seq data from human and mouse to revisit the role of transcriptional interference in the evolution of mammalian nested genes. A genomic survey reveals that whereas mammalian nested genes indeed accrued over evolutionary time, they are retained at lower frequencies than in Drosophila. Though several properties of mammalian nested genes align with observations in Drosophila and with expectations under transcriptional interference, contrary to both, their expression divergence is not statistically different from that between unnested genes, and also does not increase after nesting. Together, these results support the hypothesis that lower selection efficiencies limit rates of gene expression evolution in mammals, leading to their reliance on immediate eradication of deleterious nested genes to avoid transcriptional interference.

Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans

Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the laboratory as in nature. The base-substitution spectrum differs between C. elegans laboratory mutation accumulation (MA) experiments and the standing site-frequency spectrum, which has been argued to be in part owing to increased oxidative stress in the laboratory environment. Using genome sequence data from C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased oxidative stress, we find the base-substitution spectrum is similar between mev-1, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). Conversely, the rate of short insertions is greater in mev-1, consistent with studies in other organisms in which environmental stress increased the rate of insertion–deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are different from those of nonmononucleotide sequence, both for indels and base-substitutions, and whereas the nonmononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different, with a greater frequency of A:T → T:A transversions and an increased proportion of ±1-bp indels. The discrepancy in mutational spectra between laboratory MA experiments and natural variation is likely owing to a consistent (but unknown) effect of the laboratory environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.

Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques

Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single-nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here, we analyze patterns of CNV mutations in 32 rhesus macaque individuals from 14 parent–offspring trios. We find the rate of CNV mutations per generation is low (less than one per genome) and we observe no correlation between parental age and the number of CNVs that are passed on to offspring. We also examine segregating CNVs within the rhesus macaque sample and compare them to a similar data set from humans, finding that both species have far more segregating deletions than duplications. We contrast this with long-term patterns of gene copy-number evolution between 17 mammals, where the proportion of deletions that become fixed along the macaque lineage is much smaller than the proportion of segregating deletions. These results suggest purifying selection acting on deletions, such that the majority of them are removed from the population over time. Rhesus macaques are an important biomedical model organism, so these results will aid in our understanding of this species and the disease models it supports.

The spontaneous mutation rate of Drosophila pseudoobscura

The spontaneous mutation rate is a very variable trait that is subject to drift, selection and is sometimes highly plastic. Consequently, its variation between close species, or even between populations from the same species, can be very large. Here, I estimated the spontaneous mutation rate of Drosophila pseudoobscura and Drosophila persimilis crosses to explore the mutation rate variation within the Drosophila genus. All mutation rate estimations in Drosophila varied fourfold, probably explained by the sensitivity of the mutation rate to environmental and experimental conditions. Moreover, I found a very high mutation rate in the hybrid cross between D. pseudoobscura and D. persimilis, in agreement with known elevated mutation rate in hybrids. This mutation rate increase can be explained by heterozygosity and fitness decrease effects in hybrids.

Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs

Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus are assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: what happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases, the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference.[Gene duplication and loss; incomplete lineage sorting; multispecies coalescent; orthology; paralogy.]

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

Are Nonsynonymous Transversions Generally More Deleterious than Nonsynonymous Transitions?

It has been suggested that, due to the structure of the genetic code, nonsynonymous transitions are less likely than transversions to cause radical changes in amino acid physicochemical properties so are on average less deleterious. This view was supported by some but not all mutagenesis experiments. Because laboratory measures of fitness effects have limited sensitivities and relative frequencies of different mutations in mutagenesis studies may not match those in nature, we here revisit this issue using comparative genomics. We extend the standard codon model of sequence evolution by adding the parameter η that quantifies the ratio of the fixation probability of transitional nonsynonymous mutations to that of transversional nonsynonymous mutations. We then estimate η from the concatenated alignment of all protein-coding DNA sequences of two closely related genomes. Surprisingly, η ranges from 0.13 to 2.0 across 90 species pairs sampled from the tree of life, with 51 incidences of η < 1 and 30 incidences of η >1 that are statistically significant. Hence, whether nonsynonymous transversions are overall more deleterious than nonsynonymous transitions is species-dependent. Because the corresponding groups of amino acid replacements differ between nonsynonymous transitions and transversions, η is influenced by the relative exchangeabilities of amino acid pairs. Indeed, an extensive search reveals that the large variation in η is primarily explainable by the recently reported among-species disparity in amino acid exchangeabilities. These findings demonstrate that genome-wide nucleotide substitution patterns in coding sequences have species-specific features and are more variable among evolutionary lineages than are currently thought.

Unboxing mutations: Connecting mutation types with evolutionary consequences

A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.

Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair

We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.

The population genetics of ploidy change in unicellular fungi

Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.

Evolution of new enzymes by gene duplication and divergence

Thousands of new metabolic and regulatory enzymes have evolved by gene duplication and divergence since the dawn of life. New enzyme activities often originate from promiscuous secondary activities that have become important for fitness due to a change in the environment or a mutation. Mutations that make a promiscuous activity physiologically relevant can occur in the gene encoding the promiscuous enzyme itself, but can also occur elsewhere, resulting in increased expression of the enzyme or decreased competition between the native and novel substrates for the active site. If a newly useful activity is inefficient, gene duplication/amplification will set the stage for divergence of a new enzyme. Even a few mutations can increase the efficiency of a new activity by orders of magnitude. As efficiency increases, amplified gene arrays will shrink to provide two alleles, one encoding the original enzyme and one encoding the new enzyme. Ultimately, genomic rearrangements eliminate co-amplified genes and move newly evolved paralogs to a distant region of the genome.

Adaptation, ancestral variation and gene flow in a 'Sky Island' Drosophila species

Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south-western USA separated by large expanses of desert. Using population genomic data from more than 300 wild-caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30-100 KYA) and have recently expanded even further (0.2-2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long-term recurrent selection in these genes. In contrast, we find evidence of long-term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll-regulated antimicrobial peptides.

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.

Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps

It is increasingly evident that natural selection plays a prominent role in shaping patterns of diversity across the genome. The most commonly studied modes of natural selection are positive selection and negative selection, which refer to directional selection for and against derived mutations, respectively. Positive selection can result in hitchhiking events, in which a beneficial allele rapidly replaces all others in the population, creating a valley of diversity around the selected site along with characteristic skews in allele frequencies and linkage disequilibrium among linked neutral polymorphisms. Similarly, negative selection reduces variation not only at selected sites but also at linked sites, a phenomenon called background selection (BGS). Thus, discriminating between these two forces may be difficult, and one might expect efforts to detect hitchhiking to produce an excess of false positives in regions affected by BGS. Here, we examine the similarity between BGS and hitchhiking models via simulation. First, we show that BGS may somewhat resemble hitchhiking in simplistic scenarios in which a region constrained by negative selection is flanked by large stretches of unconstrained sites, echoing previous results. However, this scenario does not mirror the actual spatial arrangement of selected sites across the genome. By performing forward simulations under more realistic scenarios of BGS, modeling the locations of protein-coding and conserved noncoding DNA in real genomes, we show that the spatial patterns of variation produced by BGS rarely mimic those of hitchhiking events. Indeed, BGS is not substantially more likely than neutrality to produce false signatures of hitchhiking. This holds for simulations modeled after both humans and Drosophila, and for several different demographic histories. These results demonstrate that appropriately designed scans for hitchhiking need not consider BGS's impact on false-positive rates. However, we do find evidence that BGS increases the false-negative rate for hitchhiking, an observation that demands further investigation.

Short-term heritable variation overwhelms 200 generations of mutational variance for metabolic traits in Caenorhabditis elegans

Metabolic disorders have a large heritable component, and have increased markedly in human populations over the past few generations. Genome-wide association studies of metabolic traits typically find a substantial unexplained fraction of total heritability, suggesting an important role of spontaneous mutation. An alternative explanation is that epigenetic effects contribute significantly to the heritable variation. Here, we report a study designed to quantify the cumulative effects of spontaneous mutation on adenosine metabolism in the nematode Caenorhabditis elegans, including both the activity and concentration of two metabolic enzymes and the standing pools of their associated metabolites. The only prior studies on the effects of mutation on metabolic enzyme activity, in Drosophila melanogaster, found that total enzyme activity presents a mutational target similar to that of morphological and life-history traits. However, those studies were not designed to account for short-term heritable effects. We find that the short-term heritable variance for most traits is of similar magnitude as the variance among MA lines. This result suggests that the potential heritable effects of epigenetic variation in metabolic disease warrant additional scrutiny.