Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects

Unexpectedly low recombination rates and presence of hotspots in termite genomes

Meiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases in length. However, little is known about the prevalence of recombination hotspots in insect genomes. Here we infer recombination rate and its fine-scale variation across the genomes of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus We used linkage disequilibrium-based methods to infer recombination rate. We infer that recombination rates are close to 1 cM/Mb in both species, similar to the average metazoan rate. We also observe a highly punctate distribution of recombination in both termite genomes, indicative of the presence of recombination hotspots. We infer the presence of full-length PRDM9 genes in the genomes of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low recombination rates in termites indicates that eusociality is not universally connected to elevated recombination rate. We speculate that the elevated recombination rates in social Hymenoptera are instead promoted by intense selection among haploid males.

Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion

There are calls for research into the historical evolutionary relationships between humans and their commensals, as it would greatly inform models that predict the spread of pests and diseases under urban population expansion. The earliest civilizations emerged approximately 10 000 years ago and created conditions ideal for the establishment and spread of commensal urban pests. Commensal relations between humans and pests likely emerged with these early civilizations; however, for most species (e.g. German cockroach and black rat), these relationships have formed relatively recently-within the last 5000 years-raising the question of whether others could have emerged earlier. Following comparative whole genome analysis of bed bugs, Cimex lectularius, belonging to two genetically distinct lineages, one associated with bats and the other with humans, coupled with demographic modelling, our findings suggests that while their association with humans dates back potentially hundreds of thousands of years, a dramatic change in the effective population size of the human-associated lineage occurred approximately 13 000 years ago; a pattern not found in the bat-associated lineage. The timing and magnitude of the demographic patterns provide compelling evidence that the human-associated lineage closely tracked the demographic history of modern humans and their movement into the first cities. As such, bed bugs may represent the first true urban pest insect species.

Quantifying the effects of computational filter criteria on the accurate identification of de novo mutations at varying levels of sequencing coverage

The rate of spontaneous (de novo) germline mutation is a key parameter in evolutionary biology, impacting genetic diversity and contributing to the evolution of populations and species. Mutation rates themselves evolve over time but the mechanisms underlying the mutation rate variation observed across the Tree of Life remain largely to be elucidated. In recent years, whole genome sequencing has enabled the estimation of mutation rates for several organisms. However, due to a lack of community standards, many previous studies differ both empirically - most notably, in the depth of sequencing used to reliably identify de novo mutations - and computationally - utilizing different computational pipelines to detect germline mutations as well as different analysis strategies to mitigate technical artifacts - rendering comparisons between studies challenging. Using a pedigree of Western chimpanzees as an illustrative example, we here quantify the effects of commonly utilized quality metrics to reliably identify de novo mutations at different levels of sequencing coverage. We demonstrate that datasets with a mean depth of ≤ 30X are ill-suited for the detection of de novo mutations due to high false positive rates that can only be partially mitigated by computational filter criteria. In contrast, higher coverage datasets enable a comprehensive identification of de novo mutations at low false positive rates, with minimal benefits beyond a sequencing coverage of 60X, suggesting that future work should favor breadth (by sequencing additional individuals) over depth. Importantly, the simulation and analysis framework described here provides conceptual guidelines that will allow researchers to take study design and species-specific resources into account when determining computational filtering strategies for their organism of interest.

Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rates for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate, but these can be largely ameliorated through extensive manual curation. Despite these stochastic effects, manual validation of de novo mutation candidates permitted the reliable inference of pantherine mutation rates. We inferred that base pair mutation rates for all species fell between 3.6 × 10-9 and 7.6 × 10-9 per generation per base pair (mean 5.5 × 10-9 ± 1.7 × 10-9 across Pantherinae at a mean parental age of 5.5 years). Similar to other studies, we show a positive trend of mean parental age with mutation rate and our inferred rates are well within the expected range for other mammals.

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

Population genomics of seal lice provides insights into the postglacial history of northern European seals

Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.

Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus

Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.

A spatial approach to jointly estimate Wright's neighborhood size and long-term effective population size

Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume either panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested in describing the diversity of a population distributed continuously in space; this diversity is intimately linked to both the dispersal potential and the population density of the organism. A statistical model that leverages information from patterns of isolation by distance to jointly infer parameters that control local demography (such as Wright's neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wright's neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the two-form bumblebee (Bombus bifarius). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of bumblebees. The resulting inferences provide important insights into the population genetic dynamics of spatially structured populations.

Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior

Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.

Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future

Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.

Does coevolution in refugia drive mimicry in bumble bees? Insights from a South Asian mimicry group

Müllerian mimicry was proposed to be an example of a coevolved mutualism promoted by population isolation in glacial refugia. This, however, has not been well supported in butterfly models. Here, we use genomic data to test this theory while examining the population genetics behind mimetic diversification in a pair of co-mimetic bumble bees, Bombus breviceps Smith and Bombus trifasciatus Smith. In both lineages, populations were structured by geography but not as much by color pattern, suggesting sharing of color alleles across regions of restricted gene flow and formation of mimicry complexes in the absence of genetic differentiation. Demographic analyses showed mismatches between historical effective population size changes and glacial cycles, and niche modeling revealed only mild habitat retraction during glaciation. Moreover, mimetic subpopulations of the same color form in the two lineages only in some cases exhibit similar population history and genetic divergence. Therefore, the current study supports a more complex history in this comimicry than a simple refugium-coevolution model.

Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles

Body shape and size diversity and their evolutionary rates correlate with species richness at the macroevolutionary scale. However, the molecular genetic mechanisms underlying the morphological diversification across related species are poorly understood. In beetles, which account for one-fourth of the known species, adaptation to different trophic niches through morphological diversification appears to have contributed to species radiation. Here, we explored the key genes for the morphological divergence of the slender to stout body shape related to divergent feeding methods on large to small snails within the genus Carabus. We show that the zinc-finger transcription factor encoded by odd-paired (opa) controls morphological variation in the snail-feeding ground beetle Carabus blaptoides. Specifically, opa was identified as the gene underlying the slender to stout morphological difference between subspecies through genetic mapping and functional analysis via gene knockdown. Further analyses revealed that changes in opa cis-regulatory sequences likely contributed to the differences in body shape and size between C. blaptoides subspecies. Among opa cis-regulatory sequences, single nucleotide polymorphisms on the transcription factor binding sites may be associated with the morphological differences between C. blaptoides subspecies. opa was highly conserved in a wide range of taxa, especially in beetles. Therefore, opa may play an important role in adaptive morphological divergence in beetles.

Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application

Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.

Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability

Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.

Time-resolved, integrated analysis of clonally evolving genomes

Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.

'Junk' that matters: the role of transposable elements in bumblebee genome evolution

Transposable elements (TEs) are mobile DNA sequences that are widely distributed in eukaryotic genomes, where they are known to serve as a major force in genome evolution. The phenotypic impacts of TEs, while less well-studied, have also been discovered. Bumblebees are globally important pollinators in natural ecosystems and agriculture. Although TEs comprise a small fraction of bumblebee genomes, emerging evidence suggests that TEs are the major contributor of genome size variation across species and are involved in the formation of new coding and regulatory sequences. We review recent discoveries related to TEs in bumblebees, as well as outlining three key questions for the future of the field. In the future, we argue long-read sequencing technologies and genome editing techniques will help us identify TEs in bumblebees, unveil mechanisms that could account for their silencing and limited abundance, and uncover their contributions to phenotypic diversification, ecological adaptation, and speciation.

Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid

Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.

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.

Signatures of Adaptation, Constraints, and Potential Redundancy in the Canonical Immune Genes of a Key Pollinator

All organisms require an immune system to recognize, differentiate, and defend against pathogens. From an evolutionary perspective, immune systems evolve under strong selective pressures exerted by fast-evolving pathogens. However, the functional diversity of the immune system means that different immune components and their associated genes may evolve under varying forms of selection. Insect pollinators, which provide essential ecosystem services, are an important system in which to understand how selection has shaped immune gene evolution as their populations are experiencing declines with pathogens highlighted as a potential contributing factor. To improve our understanding of the genetic variation found in the immune genes of an essential pollinator, we performed whole-genome resequencing of wild-caught Bombus terrestris males. We first assessed nucleotide diversity and extended haplotype homozygosity for canonical immune genes finding the strongest signatures of positive selection acting on genes involved in pathogen recognition and antiviral defense, possibly driven by growing pathogen spread in wild populations. We also identified immune genes evolving under strong purifying selection, highlighting potential constraints on the bumblebee immune system. Lastly, we highlight the potential loss of function alleles present in the immune genes of wild-caught haploid males, suggesting that such genes are potentially less essential for development and survival and represent redundancy in the gene repertoire of the bumblebee immune system. Collectively, our analysis provides novel insights into the recent evolutionary history of the immune system of a key pollinator, highlighting targets of selection, constraints to adaptation, and potential redundancy.

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.

Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes

The globally invasive mosquito subspecies Aedes aegypti aegypti is an effective vector of human arboviruses, in part because it specializes in biting humans and breeding in human habitats. Recent work suggests that specialization first arose as an adaptation to long, hot dry seasons in the West African Sahel, where Ae. aegypti relies on human-stored water for breeding. Here, we use whole-genome cross-coalescent analysis to date the emergence of human-specialist populationsand thus further probe the climate hypothesis. Importantly, we take advantage of the known migration of specialists out of Africa during the Atlantic Slave Trade to calibrate the coalescent clock and thus obtain a more precise estimate of the older evolutionary event than would otherwise be possible. We find that human-specialist mosquitoes diverged rapidly from ecological generalists approximately 5000 years ago, at the end of the African Humid Period-a time when the Sahara dried and water stored by humans became a uniquely stable, aquatic niche in the Sahel. We also use population genomic analyses to date a previously observed influx of human-specialist alleles into major West African cities. The characteristic length of tracts of human-specialist ancestry present on a generalist genetic background in Kumasi and Ouagadougou suggests the change in behavior occurred during rapid urbanization over the last 20-40 years. Taken together, we show that the timing and ecological context of two previously observed shifts towards human biting in Ae. aegypti differ; climate was likely the original driver, but urbanization has become increasingly important in recent decades.

Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions

Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents–progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10−8 (95% confidence interval, 0.33 × 10−8–0.49 × 10−8) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments.

A caste differentiation mutant elucidates the evolution of socially parasitic ants

Most ant species have two distinct female castes-queens and workers-yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with a clonal ant, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. The prevailing theory for the evolution of these workerless social parasites is that they evolve from reproductively isolated populations of facultative intermediates that acquire parasitic phenotypes in a stepwise fashion. However, empirical evidence for such facultative ancestors remains weak, and it is unclear how reproductive isolation could gradually arise in sympatry. In contrast, we isolated these variants just a few generations after they arose within their WT parent colony, implying that the complex phenotype reported here was induced in a single genetic step. This suggests that a single genetic module can decouple the coordinated mechanisms of caste development, allowing an obligately parasitic variant to arise directly from a free-living ancestor. Consistent with this hypothesis, the variants have lost one of the two alleles of a putative supergene that is heterozygous in WTs. These findings provide a plausible explanation for the evolution of ant social parasites and implicate new candidate molecular mechanisms for ant caste differentiation.

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides an important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (N e) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate N e variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of N e through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in N e. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. N e fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater N e over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period, which matched the loss of range area near these sites; however, bottlenecks were not sufficient to erode diversity maintained during periods of large N e. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent postglacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in N e dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

Whole-genome resequencing reveals recent divergence of geographic populations of the dung beetle Phelotrupes auratus with color variation

Knowledge of population divergence history is key to understanding organism diversification mechanisms. The geotrupid dung beetle Phelotrupes auratus, which inhabits montane forests and exhibits three color forms (red, green, and indigo), diverged into five local populations (west/red, south/green, south/indigo, south/red, and east/red) in the Kinki District of Honshu, Japan, based on the combined interpretation of genetic cluster and color-form data. Here, we estimated the demographic histories of these local populations using the newly assembled draft genome sequence of P. auratus and whole-genome resequencing data obtained from each local population. Using coalescent simulation analysis, we estimated P. auratus population divergences at ca. 3800, 2100, 600, and 200 years ago, with no substantial gene flow between diverged populations, implying the existence of persistent barriers to gene flow. Notably, the last two divergence events led to three local populations with different color forms. The initial divergence may have been affected by climatic cooling around that time, and the last three divergence events may have been associated with the increasing impact of human activities. Both climatic cooling and increasing human activity may have caused habitat fragmentation and a reduction in the numbers of large mammals supplying food (dung) for P. auratus, thereby promoting the decline, segregation, and divergence of local populations. Our research demonstrates that geographic population divergence in an insect with conspicuous differences in traits such as body color may have occurred rapidly under the influence of human activity.

Rapid and predictable genome evolution across three hybrid ant populations

Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.

Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp

In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C. vestalis genome through a horizontal transfer (HT) event from a dipteran and was later transferred horizontally from C. vestalis to a lepidopteran species. Based on the phylogeny of Hel_c35, we suggested that both HTs occurred in East Asia. We have also anticipated that, as more sequenced genomes from new species become available, more HTs involving Hel_c35 would be detected. Although the inclusion of Hel_c35 as a CvBV segment turned out to be a methodological artifact, the fact that Hel_c35 copies are present in the genomes of C. vestalis and other arthropods still remains. Here, we investigated the evolution of Hel_c35 in arthropods using an updated data set to reassess our previous findings. Most species (95%) included in the present work had their genomes sequenced after our initial study was published, thus representing new descriptions of taxa harboring Hel_c35. Our results expand considerably the number of putative HTs involving Hel_c35, with up to dozens of previously undescribed events, and suggest that the most recent HTs associated with C. vestalis took place in Europe. Considering the phylogenetic distribution of Hel_c35, and the evidence that its DNA sequences are present in the calyx fluid of C. vestalis and tissues from its parasitized host, we argue that many HT events were favored by the behavior of this wasp.

Admixture of evolutionary rates across a butterfly hybrid zone

Hybridization is a major evolutionary force that can erode genetic differentiation between species, whereas reproductive isolation maintains such differentiation. In studying a hybrid zone between the swallowtail butterflies Papilio syfanius and Papilio maackii (Lepidoptera: Papilionidae), we made the unexpected discovery that genomic substitution rates are unequal between the parental species. This phenomenon creates a novel process in hybridization, where genomic regions most affected by gene flow evolve at similar rates between species, while genomic regions with strong reproductive isolation evolve at species-specific rates. Thus, hybridization mixes evolutionary rates in a way similar to its effect on genetic ancestry. Using coalescent theory, we show that the rate-mixing process provides distinct information about levels of gene flow across different parts of genomes, and the degree of rate-mixing can be predicted quantitatively from relative sequence divergence ([Formula: see text]) between the hybridizing species at equilibrium. Overall, we demonstrate that reproductive isolation maintains not only genomic differentiation, but also the rate at which differentiation accumulates. Thus, asymmetric rates of evolution provide an additional signature of loci involved in reproductive isolation.

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.

Population genomics and phylogeography of Colletes gigas , a wild bee specialized on winter flowering plants

Diet specialization may affect the population genetic structure of pollinators by reducing gene flow and driving genetic differentiation, especially in pollen‐specialist bees. Colletes gigas is a pollen‐specialist pollinator of Camellia oleifera, one of the most important staple oil crops in China. Ca. oleifera blooms in cold climates and contains special compounds that make it an unusable pollen source to other pollinators. Thus, C. gigas undoubtedly plays a key role as the main pollinator of Ca. oleifera, with biological and economic significance. Here, we use a population genomic approach to analyze the roles of geography and climate on the genetic structure, genetic diversity, and demographic history of C. gigas. A total of 1,035,407 SNPs were identified from a 582.77 Gb dataset. Clustering and phylogenetic analyses revealed a marked genetic structure, with individuals grouped into nine local clusters. A significant isolation by distance was detected by both the Mantel test (R = .866, p = .008) and linear regression (R² = .616, p < .001). Precipitation and sunshine duration were positively and significantly (R ≥ .765, p ≤ .016) correlated with observed heterozygosity (H_o) and expected heterozygosity (H_e). These results showed that C. gigas populations had a distinct phylogeographic pattern determined by geographical distance and environmental factors (precipitation and sunshine duration). In addition, an analysis of paleogeographic dynamics indicated that C. gigas populations exhibited patterns of glacial expansion and interglacial contraction, likely resulting from post‐glacial habitat contraction and fragmentation. Our results indicated that the peculiar phylogeographic patterns in C. gigas populations may be related to their specialization under long‐term adaptation to host plants. This work improves our understanding of the population genetics in pollen‐specialist bees. The distinct genetic clusters identified in this study should be taken into consideration for the protection and utilization of this specialized crop pollinator.

The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range

Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real-time, and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after being brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with the genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts. Our findings suggest that while reproductive isolation may facilitate the fixation of traits beneficial for exploiting the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.

Genomic Signatures of Recent Adaptation in a Wild Bumblebee

Environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects respond to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome affecting key processes including neurobiology and wing development. We also discover unusual features of the genome, including a region containing 53 genes that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. Overall, the genetic diversity we observe and how it is distributed throughout the genome and the population should support the resilience of this important pollinator species to ongoing and future selective pressures. Applying our approach to more species should help understand how they can differ in their adaptive potential, and to develop conservation strategies for those most at risk.

Spontaneous mutation rate estimates for the principal malaria vectors Anopheles coluzzii and Anopheles stephensi

Using high-depth whole genome sequencing of F0 mating pairs and multiple individual F1 offspring, we estimated the nuclear mutation rate per generation in the malaria vectors Anopheles coluzzii and Anopheles stephensi by detecting de novo genetic mutations. A purpose-built computer program was employed to filter actual mutations from a deep background of superficially similar artifacts resulting from read misalignment. Performance of filtering parameters was determined using software-simulated mutations, and the resulting estimate of false negative rate was used to correct final mutation rate estimates. Spontaneous mutation rates by base substitution were estimated at 1.00 × 10⁻⁹ (95% confidence interval, 2.06 × 10⁻¹⁰—2.91 × 10⁻⁹) and 1.36 × 10⁻⁹ (95% confidence interval, 4.42 × 10⁻¹⁰—3.18 × 10⁻⁹) per site per generation in A. coluzzii and A. stephensi respectively. Although similar studies have been performed on other insect species including dipterans, this is the first study to empirically measure mutation rates in the important genus Anopheles, and thus provides an estimate of µ that will be of utility for comparative evolutionary genomics, as well as for population genetic analysis of malaria vector mosquito species.

Thrice out of Asia and the adaptive radiation of the western honey bee

The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world’s most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic “hotspots.” We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.

Deleterious protein-coding variants in diverse cattle breeds of the world

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera

Background

Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae).

Results

Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3–12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species.

Conclusions

Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07987-3.

Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior

Introduced populations of invasive organisms have to cope with novel environmental challenges, while having reduced genetic variation caused by founder effects. The mechanisms associated with this "genetic paradox of invasive species" has received considerable attention, yet few studies have examined the genomic architecture of invasive species. Populations of the heart node ant Cardiocondyla obscurior belong to two distinct lineages, a New World lineage so far only found in Latin America and a more globally distributed Old World lineage. In the present study, we use population genomic approaches to compare populations of the two lineages with apparent divergent invasive potential. We find that the strong genetic differentiation of the two lineages began at least 40,000 generations ago and that activity of transposable elements (TEs) has contributed significantly to the divergence of both lineages, possibly linked to the very unusual genomic distribution of TEs in this species. Furthermore, we show that introgression from the Old World lineage is a dominant source of genetic diversity in the New World lineage, despite the lineages' strong genetic differentiation. Our study uncovers mechanisms underlying novel genetic variation in introduced populations of C. obscurior that could contribute to the species' adaptive potential.

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.

The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals

Germline mutations are the raw material for natural selection, driving species evolution and the generation of earth's biodiversity. Without this driver of genetic diversity, life on earth would stagnate. Yet, it is a double-edged sword. An excess of mutations can have devastating effects on fitness and population viability. It is therefore one of the great challenges of molecular ecology to determine the rate and mechanisms by which these mutations accrue across the tree of life. Advances in high-throughput sequencing technologies are providing new opportunities for characterizing the rates and mutational spectra within species and populations thus informing essential evolutionary parameters such as the timing of speciation events, the intricacies of historical demography, and the degree to which lineages are subject to the burdens of mutational load. Here, we will focus on both the challenge and promise of whole-genome comparisons among parents and their offspring from known pedigrees for the detection of germline mutations as they arise in a single generation. The potential of these studies is high, but the field is still in its infancy and much uncertainty remains. Namely, the technical challenges are daunting given that pedigree-based genome comparisons are essentially searching for needles in a haystack given the very low signal to noise ratio. Despite the challenges, we predict that rapidly developing methods for whole-genome comparisons hold great promise for integrating empirically derived estimates of de novo mutation rates and mutation spectra across many molecular ecological applications.

Conservation insights from wild bee genetic studies: Geographic differences, susceptibility to inbreeding, and signs of local adaptation

Conserving bees are critical both ecologically and economically. Genetic tools are valuable for monitoring these vital pollinators since tracking these small, fast-flying insects by traditional means is difficult. By surveying the current state of the literature, this review discusses how recent advances in landscape genetic and genomic research are elucidating how wild bees respond to anthropogenic threats. Current literature suggests that there may be geographic differences in the vulnerability of bee species to landscape changes. Populations of temperate bee species are becoming more isolated and more genetically depauperate as their landscape becomes more fragmented, but tropical bee species appear unaffected. These differences may be an artifact of historical differences in land-use, or it suggests that different management plans are needed for temperate and tropical bee species. Encouragingly, genetic studies on invasive bee species indicate that low levels of genetic diversity may not lead to rapid extinction in bees as once predicted. Additionally, next-generation sequencing has given researchers the power to identify potential genes under selection, which are likely critical to species' survival in their rapidly changing environment. While genetic studies provide insights into wild bee biology, more studies focusing on a greater phylogenetic and life-history breadth of species are needed. Therefore, caution should be taken when making broad conservation decisions based on the currently few species examined.

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.

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris

Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab-generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and first metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD-Seq and whole-genome re-sequencing, we localized the color-generating variant to a single SNP in the protein-coding sequence of transcription factor cut. This mutation generates an amino acid change that modifies the conformation of a coiled-coil structure outside DNA-binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non-mutant allele, indicating different mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female offspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes.

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (d_XY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure in Chironomus riparius

Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet clear. Therefore, in the present study, we propose a method coupling short-term mutation accumulation (MA) lines with subsequent whole genome sequencing (WGS) and a dedicated data analysis pipeline to investigate if chronic Cd exposure on Chironomus riparius can alter the rate at which de novo point mutations appear. Results show that Cd exposure did not affect the basal germline mutation rate nor the mutational spectrum in C. riparius, thereby arguing that exposed organisms might experience a range of other toxic effects before any mutagenic effect may occur. We show that it is possible to establish a practical and easily implemented pipeline to rapidly detect germ cell mutagens in a metazoan test organism. Furthermore, our data implicate that it is questionable to transfer mutagenicity assessments based on in vitro methods to complex metazoans.

Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale

The marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring.

Olena Maiakovska et al. provide whole-genome sequencing of the parthenogenetic and invasive marbled crayfish and develop a computational framework for data analysis of monoclonal genomes. These data and methodology allow the authors to demonstrate genetic separation between two populations and provide the first size estimate for a marbled crayfish colony, which they used to model population growth patterns.

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.

Low Spontaneous Mutation Rate and Pleistocene Radiation of Pea Aphids

Accurate estimates of divergence times are essential to understand the evolutionary history of species. It allows linking evolutionary histories of the diverging lineages with past geological, climatic, and other changes in environment and shed light on the processes involved in speciation. The pea aphid radiation includes multiple host races adapted to different legume host plants. It is thought that diversification in this system occurred very recently, over the past 8,000–16,000 years. This young age estimate was used to link diversification in pea aphids to the onset of human agriculture, and led to the establishment of the pea aphid radiation as a model system in the study of speciation with gene flow. Here, we re-examine the age of the pea aphid radiation, by combining a mutation accumulation experiment with a genome-wide estimate of divergence between distantly related pea aphid host races. We estimate the spontaneous mutation rate for pea aphids as 2.7×10-10 per haploid genome per parthenogenic generation. Using this estimate of mutation rate and the genome-wide genetic differentiation observed between pea aphid host races, we show that the pea aphid radiation is much more ancient than assumed previously, predating Neolithic agriculture by several hundreds of thousands of years. Our results rule out human agriculture as the driver of diversification of the pea aphid radiation, and call for re-assessment of the role of allopatric isolation during Pleistocene climatic oscillations in divergence of the pea aphid complex.

First Estimation of the Spontaneous Mutation Rate in Diatoms

Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10-10 and the insertion-deletion mutation rate is μid = 1.58 × 10-11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.