Selection efficiency and effective population size in Drosophila species

Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea

Insect crop pests threaten global food security. This threat is amplified through the spread of nonnative species and through adaptation of native pests to control measures. Adaptations such as pesticide resistance can result from selection on variation within a population, or through gene flow from another population. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has evolved resistance to a wide range of pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid-resistance gene CYP337B3 to South American H. zea via adaptive introgression. To understand whether this could contribute to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites. We report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4 Mbp region containing CYP337B3. Next, we identify signatures of selection in the panmictic population of nonadmixed H. zea, identifying a selective sweep at a second cytochrome P450 gene: CYP333B3. We estimate that its derived allele conferred a ∼5% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Overall, we document two mechanisms of rapid adaptation: the introduction of fitness-enhancing alleles through interspecific introgression, and selection on intraspecific variation.

The implications of satellite DNA instability on cellular function and evolution

Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.

Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus)

The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (Ne) is large or selection is particularly strong. In populations having undergone a population bottleneck, genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role.

Population-genomic analysis identifies a low rate of global adaptive fixation in the proteins of the cyclical parthenogen Daphnia magna

Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey

Coevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation by affecting the potential of local populations to respond to selection. We conducted a comparative phylogeographical study of venomous rattlesnakes and their venom-resistant ground squirrel prey across California, and assessed how effective population size (Ne) estimates correspond with a previously documented pattern of rattlesnake local adaptation. Using RAD sequencing markers, we detected lineage relationships among both the rattlesnakes (Crotalus oreganus ssp.) and ground squirrels (Otospermophilus sp.) that are incongruent with previous phylogenetic hypotheses. Both rattlesnakes and squirrels share a deep divergence at the Sacramento–San Joaquin River Delta. At this broad phylogeographical scale, we found that the locally adapted rattlesnakes had higher Ne than squirrels. At the population scale, snakes also had larger Ne accompanied by larger values of several metrics of population genetic diversity. However, the specific magnitude of local adaptation of venom activity to ground squirrel venom resistance was not significantly correlated with local differences in Ne or other diversity statistics between predator and prey populations, suggesting that other factors in the geographic mosaic of coevolution contribute to the specific local-scale outcomes of this interaction. These results suggest an evolutionary mechanism that may explain some (but clearly not all) of rattlesnake local adaptation in this coevolutionary interaction – larger population sizes raise the adaptive potential of rattlesnakes compared to ground squirrels.

Limited divergent adaptation despite a substantial environmental cline in wild pea

Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.

The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface

The red palm weevil, Rhynchophorus ferrugineus, infests palm plantations, leading to large financial losses and soil erosion. Pest-host interactions are poorly understood in R. ferrugineus, but the analysis of genetic diversity and pest origins will help advance efforts to eradicate this pest. We sequenced the genome of R. ferrugineus using a combination of paired-end Illumina sequencing (150 bp), Oxford Nanopore long reads, 10X Genomics and synteny analysis to produce an assembly with a scaffold N50 of ~60 Mb. Structural variations showed duplication of detoxifying and insecticide resistance genes (e.g., glutathione S-transferase, P450, Rdl). Furthermore, the evolution of gene families identified those under positive selection including one glycosyl hydrolase (GH16) gene family, which appears to result from horizontal gene transfer. This genome will be a valuable resource to understand insect evolution and behavior and to allow the genetic modification of key genes that will help control this pest.

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Background

In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (N_e), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.

Results

We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high N_e estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N_e, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.

Conclusions

Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization

Evolutionary studies over the last several decades have invoked fitness trade-offs to explain why species prefer some environments to others. However, the effects of population size on trade-offs and ecological specialization remain largely unknown. To complicate matters, trade-offs themselves have been visualized in multiple ways in the literature. Thus, it is not clear how population size can affect the various aspects of trade-offs. To address these issues, we conducted experimental evolution with Escherichia coli populations of two different sizes in two nutritionally limited environments, and studied fitness trade-offs from three different perspectives. We found that larger populations evolved greater fitness trade-offs, regardless of how trade-offs are conceptualized. Moreover, although larger populations adapted more to their selection conditions, they also became more maladapted to other environments, ultimately paying heavier costs of adaptation. To enhance the generalizability of our results, we further investigated the evolution of ecological specialization across six different environmental pairs, and found that larger populations specialized more frequently and evolved consistently steeper reaction norms of fitness. This is the first study to demonstrate a relationship between population size and fitness trade-offs, and the results are important in understanding the population genetics of ecological specialization and vulnerability to environmental changes.

Adapting in larger numbers can increase the vulnerability of Escherichia coli populations to environmental changes

Larger populations generally adapt faster to their existing environment. However, it is unknown if the population size experienced during evolution influences the ability to face sudden environmental changes. To investigate this issue, we subjected replicate Escherichia coli populations of different sizes to experimental evolution in an environment containing a cocktail of three antibiotics. In this environment, the ability to actively efflux molecules outside the cell is expected to be a major fitness-affecting trait. We found that all the populations eventually reached similar fitness in the antibiotic cocktail despite adapting at different speeds, with the larger populations adapting faster. Surprisingly, although efflux activity (EA) enhanced in the smaller populations, it decayed in the larger ones. The evolution of EA was largely shaped by pleiotropic responses to selection and not by drift. This demonstrates that quantitative differences in population size can lead to qualitative differences (decay/enhancement) in the fate of a character during adaptation to identical environments. Furthermore, the larger populations showed inferior fitness upon sudden exposure to several alternative stressful environments. These observations provide a novel link between population size and vulnerability to environmental changes. Counterintuitively, adapting in larger numbers can render bacterial populations more vulnerable to abrupt environmental changes.

Selection shapes turnover and magnitude of sex-biased expression in Drosophila gonads

BACKGROUND

Sex-biased gene expression is thought to drive the phenotypic differences in males and females in metazoans. Drosophila has served as a primary model for studying male-female differences in gene expression, and its effects on protein sequence divergence. However, the forces shaping evolution of sex-biased expression remain largely unresolved, including the roles of selection and pleiotropy. Research on sex organs in Drosophila, employing original approaches and multiple-species contrasts, provides a means to gain insights into factors shaping the turnover and magnitude (fold-bias) of sex-biased expression.

RESULTS

Here, using recent RNA-seq data, we studied sex-biased gonadal expression in 10,740 protein coding sequences in four species of Drosophila, D. melanogaster, D. simulans, D. yakuba and D. ananassae (5 to 44 My divergence). Using an approach wherein we identified genes with lineage-specific transitions (LSTs) in sex-biased status (amongst testis-biased, ovary-biased and unbiased; thus, six transition types) standardized to the number of genes with the ancestral state (S-LSTs), and those with clade-wide expression bias status, we reveal several key findings. First, the six categorical types of S-LSTs in sex-bias showed disparate rates of turnover, consistent with differential selection pressures. Second, the turnover in sex-biased status was largely unrelated to cross-tissue expression breadth, suggesting pleiotropy does not restrict evolution of sex-biased expression. Third, the fold-sex-biased expression, for both testis-biased and ovary-biased genes, evolved directionally over time toward higher values, a crucial finding that could be interpreted as a selective advantage of greater sex-bias, and sexual antagonism. Fourth, in terms of protein divergence, genes with LSTs to testis-biased expression exhibited weak signals of elevated rates of evolution (than ovary-biased) in as little as 5 My, which strengthened over time. Moreover, genes with clade-wide testis-specific expression (44 My), a status not observed for any ovary-biased genes, exhibited striking acceleration of protein divergence, which was linked to low pleiotropy.

CONCLUSIONS

By studying LSTs and clade-wide sex-biased gonadal expression in a multi-species clade of Drosophila, we describe evidence that interspecies turnover and magnitude of sex-biased expression have been influenced by selection. Further, whilst pleiotropy was not connected to turnover in sex-biased gonadal expression, it likely explains protein sequence divergence.

Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii

The mutational patterns of large tandem arrays of short sequence repeats remain largely unknown, despite observations of their high levels of variation in sequence and genomic abundance within and between species. Many factors can influence the dynamics of tandem repeat evolution; however, their evolution has only been examined over a limited phylogenetic sample of taxa. Here, we use publicly available whole-genome sequencing data of 85 haploid mutation accumulation lines derived from six geographically diverse Chlamydomonas reinhardtii isolates to investigate genome-wide mutation rates and patterns in tandem repeats in this species. We find that tandem repeat composition differs among ancestral strains, both in genome-wide abundance and presence/absence of individual repeats. Estimated mutation rates (repeat copy number expansion and contraction) were high, averaging 4.3×10⁻⁴ per generation per single unit copy. Although orders of magnitude higher than other types of mutation previously reported in C. reinhardtii, these tandem repeat mutation rates were one order of magnitude lower than what has recently been found in Daphnia pulex, even after correcting for lower overall genome-wide satellite abundance in C. reinhardtii. Most high-abundance repeats were related to others by a single mutational step. Correlations of repeat copy number changes within genomes revealed clusters of closely related repeats that were strongly correlated positively or negatively, and similar patterns of correlation arose independently in two different mutation accumulation experiments. Together, these results paint a dynamic picture of tandem repeat evolution in this unicellular alga.

De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs

Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.

Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes

Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species.

Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources

Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6–78.6) in comparison to the field populations (point estimate range 118.9–580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F_st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F_st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (F_SC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.

Contribution of nonohnologous duplicated genes to high habitat variability in mammals

The mechanism by which genetic systems affect environmental adaptation is a focus of considerable attention in the fields of ecology, evolution, and conservation. However, the genomic characteristics that constrain adaptive evolution have remained unknown. A recent study showed that the proportion of duplicated genes in whole Drosophila genomes correlated with environmental variability within habitat, but it remains unclear whether the correlation is observed even in vertebrates whose genomes including a large number of duplicated genes generated by whole-genome duplication (WGD). Here, we focus on fully sequenced mammalian genomes that experienced WGD in early vertebrate lineages and show that the proportion of small-scale duplication (SSD) genes in the genome, but not that of WGD genes, is significantly correlated with habitat variability. Moreover, species with low habitat variability have a higher proportion of lost duplicated genes, particularly SSD genes, than those with high habitat variability. These results indicate that species that inhabit variable environments may maintain more SSD genes in their genomes and suggest that SSD genes are important for adapting to novel environments and surviving environmental changes. These insights may be applied to predicting invasive and endangered species.

Population size and the rate of evolution

Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (Ne) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood.

Molecular evolution and the latitudinal biodiversity gradient

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Molecular hyperdiversity and evolution in very large populations

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements.

Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera

Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution.

Habitat variability correlates with duplicate content of Drosophila genomes

The factors limiting the habitat range of species are crucial in understanding their biodiversity and response to environmental change. Yet the genetic and genomic architectures that produce genetic variation to enable environmental adaptation have remained poorly understood. Here we show that the proportion of duplicated genes (P_D) in the whole genomes of fully sequenced Drosophila species is significantly correlated with environmental variability within the habitats measured by the climatic envelope and habitat diversity. Furthermore, species with a low P_D tend to lose the duplicated genes owing to their faster evolution. These results indicate that the rapid relaxation of functional constraints on duplicated genes resulted in a low P_D for species with lower habitat diversity, and suggest that the maintenance of duplicated genes gives organisms an ecological advantage during evolution. We therefore propose that the P_D in a genome is related to adaptation to environmental variation.

DNA barcoding of recently diverged species: relative performance of matching methods

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race

BACKGROUND

Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencing pathway also plays a crucial role in limiting TE proliferation. How these two forces jointly determine TE abundance is not well understood. To shed light on the nature of factors that predict TE success, we test three distinct hypotheses in the Drosophila genus. First, we determine whether TE abundance and relaxed genome-wide purifying selection on protein sequences are positively correlated. This serves to test the hypothesis that variation in TE abundance in the Drosophila genus can be explained by the strength of natural selection, relative to drift, acting in parallel against mildly deleterious non-synonymous mutations. Second, we test whether increasing TE abundance is correlated with an increased rate of amino-acid evolution in genes encoding the piRNA machinery, as might be predicted by an evolutionary arms race model. Third, we test whether increasing TE abundance is correlated with greater codon bias in genes of the piRNA machinery. This is predicted if increasing TE abundance selects for increased efficiency in the machinery of genome defense.

RESULTS

Surprisingly, we find neither of the first two hypotheses to be true. Specifically, we found that genome-wide levels of purifying selection, measured by the ratio of non-synonymous to synonymous substitution rates (ω), were greater in species with greater TE abundance. In addition, species with greater TE abundance have greater levels of purifying selection in the piRNA machinery. In contrast, it appears that increasing TE abundance has primarily driven adaptation in the piRNA machinery by increasing codon bias.

CONCLUSIONS

These results indicate that within the Drosophila genus, a historically reduced strength of selection relative to drift is unlikely to explain patterns of increased TE success across species. Other factors, such as ecological exposure, are likely to contribute to variation in TE abundances within species. Furthermore, constraints on the piRNA machinery may temper the evolutionary arms race that would drive increasing rates of evolution at the amino acid level. In the face of these constraints, selection may act primarily by improving the translational efficiency of the machinery of genome defense through efficient codon usage.

Natural selection on functional modules, a genome-wide analysis

Classically, the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes. The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation. This approach, which assumed independence among genes, has not been able to identify biological functions significantly enriched in positively selected genes in individual species. Alternatively, pooling related species has enhanced the search for signatures of selection. However, grouping signatures does not allow testing for adaptive differences between species. Here we introduce the Gene-Set Selection Analysis (GSSA), a new genome-wide approach to test for evidences of natural selection on functional modules. GSSA is able to detect lineage specific evolutionary rate changes in a notable number of functional modules. For example, in nine mammal and Drosophilae genomes GSSA identifies hundreds of functional modules with significant associations to high and low rates of evolution. Many of the detected functional modules with high evolutionary rates have been previously identified as biological functions under positive selection. Notably, GSSA identifies conserved functional modules with many positively selected genes, which questions whether they are exclusively selected for fitting genomes to environmental changes. Our results agree with previous studies suggesting that adaptation requires positive selection, but not every mutation under positive selection contributes to the adaptive dynamical process of the evolution of species.

Mutation bias favors protein folding stability in the evolution of small populations

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction.

Mutation bias favors protein folding stability in the evolution of small populations

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction.

The efficiency of purifying selection in Mammals vs. Drosophila for metabolic genes

The nearly neutral theory of molecular evolution states that the efficiency of natural selection depends on the effective population size. By using a wide range of multispecies data on nucleotide polymorphism, we have tried to ascertain whether there are any differences in the level of selective constraints of metabolic process genes between Mammals and Drosophila species. The results are consistent with a higher selective constraint in Drosophila than in Mammals, according to the expected under the nearly neutral model: purifying selection seems to be more efficient in species with a larger effective population size.

Why do species vary in their rate of molecular evolution?

Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses.

Effective population size and the rate and pattern of nucleotide substitutions

Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size (N(e)). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N(e) is often substantial, however, and must be accounted for in analyses of molecular evolution.